Starting phenix.real_space_refine on Fri Mar 22 14:48:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjv_10513/03_2024/6tjv_10513_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjv_10513/03_2024/6tjv_10513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjv_10513/03_2024/6tjv_10513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjv_10513/03_2024/6tjv_10513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjv_10513/03_2024/6tjv_10513_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjv_10513/03_2024/6tjv_10513_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 12 7.16 5 Zn 1 6.06 5 P 2 5.49 5 Mg 1 5.21 5 S 170 5.16 5 C 22358 2.51 5 N 5403 2.21 5 O 5891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D GLU 350": "OE1" <-> "OE2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ARG 432": "NH1" <-> "NH2" Residue "D ARG 441": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "E ARG 25": "NH1" <-> "NH2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F GLU 246": "OE1" <-> "OE2" Residue "F GLU 403": "OE1" <-> "OE2" Residue "F GLU 441": "OE1" <-> "OE2" Residue "F PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 476": "NH1" <-> "NH2" Residue "F PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 41": "OE1" <-> "OE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H GLU 271": "OE1" <-> "OE2" Residue "H GLU 292": "OE1" <-> "OE2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I GLU 122": "OE1" <-> "OE2" Residue "I GLU 125": "OE1" <-> "OE2" Residue "I ARG 179": "NH1" <-> "NH2" Residue "J ARG 17": "NH1" <-> "NH2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J ARG 45": "NH1" <-> "NH2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "K GLU 21": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "K TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "K ARG 174": "NH1" <-> "NH2" Residue "L ARG 35": "NH1" <-> "NH2" Residue "L ARG 72": "NH1" <-> "NH2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M GLU 55": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "N GLU 14": "OE1" <-> "OE2" Residue "N ARG 32": "NH1" <-> "NH2" Residue "N ARG 35": "NH1" <-> "NH2" Residue "N ARG 136": "NH1" <-> "NH2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "P ARG 26": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 103": "NH1" <-> "NH2" Residue "P GLU 117": "OE1" <-> "OE2" Residue "P ARG 126": "NH1" <-> "NH2" Residue "P ARG 135": "NH1" <-> "NH2" Residue "P GLU 139": "OE1" <-> "OE2" Residue "P GLU 213": "OE1" <-> "OE2" Residue "P GLU 262": "OE1" <-> "OE2" Residue "P GLU 278": "OE1" <-> "OE2" Residue "P GLU 399": "OE1" <-> "OE2" Residue "P ARG 417": "NH1" <-> "NH2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q ARG 84": "NH1" <-> "NH2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "Q GLU 117": "OE1" <-> "OE2" Residue "S GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33838 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2780 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3541 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 456} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "C" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3615 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 455} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 769 Classifications: {'peptide': 100} Link IDs: {'TRANS': 99} Chain: "F" Number of atoms: 4587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4587 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 567} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1262 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 160} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3153 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 370} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1520 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 180} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1278 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 11, 'TRANS': 144} Chain: "K" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1594 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 184} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 609 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "M" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 879 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "N" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1160 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 11, 'TRANS': 135} Chain: "O" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "P" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3496 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 30, 'TRANS': 395} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "Q" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1095 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 136} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 432 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'DGD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'PGT': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'BCR': 1, 'CLA': 1, 'SQD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'SF4': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 120 Unusual residues: {'DGD': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21442 SG CYS I 103 49.246 52.665 40.882 1.00 40.28 S ATOM 21486 SG CYS I 109 44.489 50.333 36.333 1.00 40.71 S ATOM 21195 SG CYS I 73 42.399 52.392 43.205 1.00 39.24 S ATOM 21467 SG CYS I 106 45.467 46.791 42.412 1.00 42.47 S ATOM 21142 SG CYS I 66 33.780 51.881 32.070 1.00 48.55 S ATOM 21164 SG CYS I 69 39.151 54.232 35.712 1.00 42.88 S ATOM 21123 SG CYS I 63 38.075 57.079 29.652 1.00 52.65 S ATOM 21520 SG CYS I 113 39.997 50.003 29.718 1.00 46.46 S ATOM 24507 SG CYS K 148 51.974 48.622 47.699 1.00 45.35 S ATOM 23783 SG CYS K 53 58.474 49.141 49.919 1.00 48.57 S ATOM 23777 SG CYS K 52 54.568 44.698 53.408 1.00 49.73 S ATOM 24281 SG CYS K 117 52.006 51.666 52.466 1.00 40.88 S Time building chain proxies: 17.90, per 1000 atoms: 0.53 Number of scatterers: 33838 At special positions: 0 Unit cell: (140.4, 98.55, 238.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 12 26.01 S 170 16.00 P 2 15.00 Mg 1 11.99 O 5891 8.00 N 5403 7.00 C 22358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.82 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 73 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 103 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 106 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 69 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 113 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 66 " pdb=" SF4 K 501 " pdb="FE2 SF4 K 501 " - pdb=" SG CYS K 53 " pdb="FE4 SF4 K 501 " - pdb=" SG CYS K 117 " pdb="FE1 SF4 K 501 " - pdb=" SG CYS K 148 " pdb="FE3 SF4 K 501 " - pdb=" SG CYS K 52 " Number of angles added : 36 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB PRO F 36 " Number of C-beta restraints generated: 7908 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 178 helices and 15 sheets defined 53.9% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.83 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 Processing helix chain 'A' and resid 22 through 27 removed outlier: 3.585A pdb=" N LYS A 26 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 22 through 27' Processing helix chain 'A' and resid 30 through 59 removed outlier: 3.989A pdb=" N LEU A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.617A pdb=" N LEU A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 Proline residue: A 103 - end of helix removed outlier: 4.015A pdb=" N VAL A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Proline residue: A 109 - end of helix removed outlier: 3.516A pdb=" N SER A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 4.047A pdb=" N SER A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.528A pdb=" N GLY A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.711A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 215 through 224 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.719A pdb=" N THR A 247 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 248' Processing helix chain 'A' and resid 252 through 260 removed outlier: 3.844A pdb=" N PHE A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 removed outlier: 4.030A pdb=" N SER A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 303 through 330 removed outlier: 3.652A pdb=" N LYS A 317 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TRP A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 365 Processing helix chain 'B' and resid 15 through 18 Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.504A pdb=" N ASP B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 61 removed outlier: 3.853A pdb=" N MET B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE B 59 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Proline residue: B 60 - end of helix Processing helix chain 'B' and resid 78 through 97 removed outlier: 3.541A pdb=" N LEU B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 110 through 128 removed outlier: 3.973A pdb=" N ILE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 150 removed outlier: 3.569A pdb=" N ALA B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 187 removed outlier: 3.605A pdb=" N ALA B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 206 through 223 removed outlier: 3.760A pdb=" N GLY B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 241 through 263 removed outlier: 3.507A pdb=" N VAL B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 294 removed outlier: 3.664A pdb=" N ASN B 290 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 316 removed outlier: 3.845A pdb=" N ILE B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 353 removed outlier: 3.875A pdb=" N LEU B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 362 Processing helix chain 'B' and resid 365 through 368 No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 370 through 384 removed outlier: 3.699A pdb=" N LEU B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS B 379 " --> pdb=" O GLY B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 408 through 434 removed outlier: 3.665A pdb=" N LEU B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 428 " --> pdb=" O TYR B 424 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 429 " --> pdb=" O TYR B 425 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 473 removed outlier: 3.791A pdb=" N MET B 466 " --> pdb=" O VAL B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 removed outlier: 4.121A pdb=" N ASN B 483 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU B 484 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP B 490 " --> pdb=" O THR B 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 42 removed outlier: 3.630A pdb=" N VAL C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) Proline residue: C 33 - end of helix removed outlier: 4.186A pdb=" N ALA C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 96 removed outlier: 4.686A pdb=" N MET C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE C 77 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL C 80 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 83 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 88 " --> pdb=" O ASP C 85 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 92 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Proline residue: C 93 - end of helix removed outlier: 3.669A pdb=" N VAL C 96 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 101 No H-bonds generated for 'chain 'C' and resid 98 through 101' Processing helix chain 'C' and resid 105 through 125 Processing helix chain 'D' and resid 11 through 25 Proline residue: D 18 - end of helix Processing helix chain 'D' and resid 30 through 53 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 84 through 102 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 111 through 127 removed outlier: 3.571A pdb=" N LEU D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 152 removed outlier: 4.229A pdb=" N VAL D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Proline residue: D 145 - end of helix Processing helix chain 'D' and resid 158 through 185 removed outlier: 3.526A pdb=" N SER D 172 " --> pdb=" O TYR D 168 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 218 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 240 through 264 Processing helix chain 'D' and resid 267 through 294 removed outlier: 3.621A pdb=" N ALA D 271 " --> pdb=" O PRO D 267 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 276 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE D 279 " --> pdb=" O GLY D 275 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 318 removed outlier: 3.614A pdb=" N TYR D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL D 313 " --> pdb=" O HIS D 309 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 314 " --> pdb=" O MET D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 353 removed outlier: 3.647A pdb=" N ALA D 328 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 385 removed outlier: 3.619A pdb=" N ALA D 376 " --> pdb=" O PRO D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 404 Processing helix chain 'D' and resid 409 through 433 Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 454 through 468 removed outlier: 3.768A pdb=" N LEU D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 468 " --> pdb=" O VAL D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 474 Processing helix chain 'D' and resid 478 through 486 Processing helix chain 'E' and resid 3 through 23 Processing helix chain 'E' and resid 27 through 51 removed outlier: 4.041A pdb=" N LEU E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 88 removed outlier: 3.619A pdb=" N ALA E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'F' and resid 9 through 26 Proline residue: F 13 - end of helix removed outlier: 4.566A pdb=" N SER F 16 " --> pdb=" O PRO F 13 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET F 20 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL F 21 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU F 22 " --> pdb=" O GLY F 19 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER F 23 " --> pdb=" O MET F 20 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 24 " --> pdb=" O VAL F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 61 Processing helix chain 'F' and resid 89 through 112 removed outlier: 3.644A pdb=" N GLY F 111 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 138 removed outlier: 3.527A pdb=" N GLY F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 160 removed outlier: 3.728A pdb=" N VAL F 148 " --> pdb=" O PHE F 144 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU F 149 " --> pdb=" O ASN F 145 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR F 153 " --> pdb=" O LEU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 193 removed outlier: 3.738A pdb=" N ARG F 174 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY F 183 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU F 188 " --> pdb=" O ASP F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 198 No H-bonds generated for 'chain 'F' and resid 195 through 198' Processing helix chain 'F' and resid 205 through 211 Processing helix chain 'F' and resid 217 through 234 Proline residue: F 231 - end of helix Processing helix chain 'F' and resid 242 through 246 Processing helix chain 'F' and resid 254 through 260 removed outlier: 4.472A pdb=" N ASN F 259 " --> pdb=" O SER F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 Processing helix chain 'F' and resid 274 through 279 removed outlier: 3.811A pdb=" N LEU F 279 " --> pdb=" O PRO F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 304 removed outlier: 3.631A pdb=" N ALA F 304 " --> pdb=" O LEU F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 329 removed outlier: 3.779A pdb=" N VAL F 323 " --> pdb=" O TYR F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 359 removed outlier: 4.072A pdb=" N LEU F 340 " --> pdb=" O PHE F 336 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR F 341 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 390 removed outlier: 3.645A pdb=" N PHE F 382 " --> pdb=" O SER F 378 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU F 389 " --> pdb=" O GLY F 385 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 410 removed outlier: 3.732A pdb=" N GLN F 401 " --> pdb=" O SER F 397 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU F 403 " --> pdb=" O PHE F 399 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU F 404 " --> pdb=" O PRO F 400 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU F 405 " --> pdb=" O GLN F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 437 removed outlier: 3.734A pdb=" N THR F 424 " --> pdb=" O LEU F 420 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA F 427 " --> pdb=" O ASN F 423 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU F 430 " --> pdb=" O ALA F 426 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL F 437 " --> pdb=" O THR F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 446 No H-bonds generated for 'chain 'F' and resid 444 through 446' Processing helix chain 'F' and resid 454 through 476 Proline residue: F 459 - end of helix removed outlier: 3.606A pdb=" N LEU F 466 " --> pdb=" O VAL F 462 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL F 467 " --> pdb=" O ASP F 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU F 468 " --> pdb=" O LEU F 464 " (cutoff:3.500A) Proline residue: F 471 - end of helix removed outlier: 3.801A pdb=" N ALA F 475 " --> pdb=" O PRO F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 508 removed outlier: 4.250A pdb=" N ALA F 492 " --> pdb=" O ALA F 488 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU F 493 " --> pdb=" O THR F 489 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR F 494 " --> pdb=" O ALA F 490 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE F 495 " --> pdb=" O ALA F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 528 removed outlier: 3.658A pdb=" N ASN F 526 " --> pdb=" O PRO F 522 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU F 527 " --> pdb=" O SER F 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 541 Proline residue: F 535 - end of helix removed outlier: 4.325A pdb=" N ARG F 539 " --> pdb=" O LYS F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 577 removed outlier: 3.543A pdb=" N TRP F 555 " --> pdb=" O ARG F 551 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL F 561 " --> pdb=" O ASP F 557 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP F 562 " --> pdb=" O ARG F 558 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE F 568 " --> pdb=" O THR F 564 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY F 569 " --> pdb=" O GLY F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 582 No H-bonds generated for 'chain 'F' and resid 580 through 582' Processing helix chain 'F' and resid 587 through 597 Processing helix chain 'G' and resid 3 through 28 removed outlier: 3.639A pdb=" N VAL G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 53 removed outlier: 3.803A pdb=" N GLY G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 70 through 81 Processing helix chain 'G' and resid 94 through 117 Processing helix chain 'G' and resid 131 through 140 removed outlier: 3.649A pdb=" N ILE G 135 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE G 140 " --> pdb=" O GLY G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 165 removed outlier: 4.109A pdb=" N SER G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 55 Processing helix chain 'H' and resid 60 through 69 Proline residue: H 65 - end of helix removed outlier: 4.347A pdb=" N SER H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG H 69 " --> pdb=" O PRO H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 90 Proline residue: H 86 - end of helix removed outlier: 3.712A pdb=" N LEU H 89 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 124 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 130 through 137 removed outlier: 3.792A pdb=" N PHE H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG H 136 " --> pdb=" O PHE H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 148 removed outlier: 3.580A pdb=" N LEU H 144 " --> pdb=" O TYR H 140 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA H 147 " --> pdb=" O ASP H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 193 removed outlier: 4.645A pdb=" N VAL H 173 " --> pdb=" O TYR H 170 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR H 174 " --> pdb=" O GLY H 171 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU H 184 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Proline residue: H 185 - end of helix removed outlier: 4.014A pdb=" N TYR H 190 " --> pdb=" O VAL H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 203 Processing helix chain 'H' and resid 212 through 217 removed outlier: 3.553A pdb=" N ASN H 217 " --> pdb=" O GLU H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 228 removed outlier: 4.013A pdb=" N SER H 228 " --> pdb=" O MET H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 282 removed outlier: 3.695A pdb=" N VAL H 273 " --> pdb=" O MET H 269 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS H 274 " --> pdb=" O ARG H 270 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP H 281 " --> pdb=" O ARG H 277 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY H 282 " --> pdb=" O GLN H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 297 Processing helix chain 'H' and resid 303 through 305 No H-bonds generated for 'chain 'H' and resid 303 through 305' Processing helix chain 'H' and resid 307 through 309 No H-bonds generated for 'chain 'H' and resid 307 through 309' Processing helix chain 'H' and resid 358 through 362 Processing helix chain 'H' and resid 364 through 366 No H-bonds generated for 'chain 'H' and resid 364 through 366' Processing helix chain 'H' and resid 368 through 370 No H-bonds generated for 'chain 'H' and resid 368 through 370' Processing helix chain 'H' and resid 376 through 384 removed outlier: 4.020A pdb=" N VAL H 379 " --> pdb=" O ALA H 376 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA H 380 " --> pdb=" O ASP H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 391 No H-bonds generated for 'chain 'H' and resid 389 through 391' Processing helix chain 'I' and resid 4 through 33 removed outlier: 3.592A pdb=" N GLN I 16 " --> pdb=" O LYS I 12 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET I 32 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG I 33 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 43 No H-bonds generated for 'chain 'I' and resid 41 through 43' Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 108 through 112 Processing helix chain 'I' and resid 131 through 133 No H-bonds generated for 'chain 'I' and resid 131 through 133' Processing helix chain 'I' and resid 148 through 150 No H-bonds generated for 'chain 'I' and resid 148 through 150' Processing helix chain 'I' and resid 160 through 162 No H-bonds generated for 'chain 'I' and resid 160 through 162' Processing helix chain 'I' and resid 184 through 192 Processing helix chain 'J' and resid 46 through 55 Processing helix chain 'J' and resid 120 through 128 Processing helix chain 'J' and resid 162 through 164 No H-bonds generated for 'chain 'J' and resid 162 through 164' Processing helix chain 'K' and resid 26 through 40 removed outlier: 3.512A pdb=" N VAL K 34 " --> pdb=" O SER K 30 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG K 39 " --> pdb=" O TYR K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 61 removed outlier: 3.937A pdb=" N GLU K 56 " --> pdb=" O CYS K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 103 removed outlier: 3.786A pdb=" N LEU K 101 " --> pdb=" O ALA K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 118 No H-bonds generated for 'chain 'K' and resid 116 through 118' Processing helix chain 'K' and resid 122 through 124 No H-bonds generated for 'chain 'K' and resid 122 through 124' Processing helix chain 'K' and resid 135 through 137 No H-bonds generated for 'chain 'K' and resid 135 through 137' Processing helix chain 'K' and resid 152 through 168 removed outlier: 3.591A pdb=" N MET K 156 " --> pdb=" O PRO K 152 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP K 157 " --> pdb=" O GLU K 153 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS K 165 " --> pdb=" O LYS K 161 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN K 168 " --> pdb=" O LYS K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 173 No H-bonds generated for 'chain 'K' and resid 171 through 173' Processing helix chain 'K' and resid 205 through 207 No H-bonds generated for 'chain 'K' and resid 205 through 207' Processing helix chain 'L' and resid 5 through 21 removed outlier: 3.959A pdb=" N LEU L 10 " --> pdb=" O GLU L 6 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY L 18 " --> pdb=" O GLY L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 34 Processing helix chain 'L' and resid 41 through 60 Proline residue: L 56 - end of helix removed outlier: 3.746A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'M' and resid 43 through 57 Processing helix chain 'M' and resid 67 through 87 removed outlier: 3.603A pdb=" N ASP M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 16 Processing helix chain 'N' and resid 31 through 40 removed outlier: 3.501A pdb=" N LYS N 40 " --> pdb=" O ARG N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 89 removed outlier: 3.659A pdb=" N GLU N 89 " --> pdb=" O THR N 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 85 through 89' Processing helix chain 'N' and resid 105 through 107 No H-bonds generated for 'chain 'N' and resid 105 through 107' Processing helix chain 'N' and resid 110 through 121 removed outlier: 3.693A pdb=" N THR N 120 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 33 No H-bonds generated for 'chain 'O' and resid 31 through 33' Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'P' and resid 21 through 28 removed outlier: 3.936A pdb=" N ARG P 26 " --> pdb=" O ASP P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 67 removed outlier: 3.724A pdb=" N LYS P 43 " --> pdb=" O VAL P 39 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE P 44 " --> pdb=" O ASN P 40 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE P 53 " --> pdb=" O LYS P 49 " (cutoff:3.500A) Proline residue: P 54 - end of helix removed outlier: 3.984A pdb=" N ARG P 60 " --> pdb=" O ASP P 56 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU P 63 " --> pdb=" O TRP P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 85 No H-bonds generated for 'chain 'P' and resid 83 through 85' Processing helix chain 'P' and resid 110 through 118 Processing helix chain 'P' and resid 126 through 131 Processing helix chain 'P' and resid 138 through 148 removed outlier: 3.595A pdb=" N GLU P 142 " --> pdb=" O GLU P 139 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP P 143 " --> pdb=" O PHE P 140 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET P 148 " --> pdb=" O ALA P 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 160 No H-bonds generated for 'chain 'P' and resid 157 through 160' Processing helix chain 'P' and resid 166 through 177 Processing helix chain 'P' and resid 182 through 190 Processing helix chain 'P' and resid 196 through 228 removed outlier: 4.322A pdb=" N VAL P 214 " --> pdb=" O LEU P 210 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET P 215 " --> pdb=" O PHE P 211 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA P 216 " --> pdb=" O TRP P 212 " (cutoff:3.500A) Proline residue: P 217 - end of helix removed outlier: 3.751A pdb=" N SER P 223 " --> pdb=" O PHE P 219 " (cutoff:3.500A) Processing helix chain 'P' and resid 234 through 247 Processing helix chain 'P' and resid 269 through 271 No H-bonds generated for 'chain 'P' and resid 269 through 271' Processing helix chain 'P' and resid 275 through 278 No H-bonds generated for 'chain 'P' and resid 275 through 278' Processing helix chain 'P' and resid 281 through 287 removed outlier: 3.553A pdb=" N ALA P 286 " --> pdb=" O PRO P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 332 through 339 removed outlier: 4.151A pdb=" N GLN P 338 " --> pdb=" O LEU P 335 " (cutoff:3.500A) Processing helix chain 'P' and resid 346 through 353 removed outlier: 3.592A pdb=" N TYR P 351 " --> pdb=" O TYR P 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 389 Processing helix chain 'P' and resid 399 through 415 removed outlier: 3.795A pdb=" N ASN P 404 " --> pdb=" O HIS P 400 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE P 415 " --> pdb=" O GLN P 411 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 17 through 23 Processing helix chain 'Q' and resid 51 through 58 Processing helix chain 'Q' and resid 61 through 71 Processing helix chain 'Q' and resid 79 through 85 Processing sheet with id= A, first strand: chain 'D' and resid 66 through 68 removed outlier: 3.776A pdb=" N GLU D 66 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 69 through 74 removed outlier: 7.056A pdb=" N LEU F 81 " --> pdb=" O TRP F 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 11 through 14 removed outlier: 4.028A pdb=" N ASP H 39 " --> pdb=" O THR H 31 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 327 through 332 removed outlier: 3.519A pdb=" N LEU H 342 " --> pdb=" O HIS H 327 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS H 354 " --> pdb=" O TYR H 341 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'I' and resid 56 through 58 Processing sheet with id= F, first strand: chain 'I' and resid 79 through 82 Processing sheet with id= G, first strand: chain 'J' and resid 38 through 40 removed outlier: 6.927A pdb=" N ARG J 95 " --> pdb=" O ILE J 39 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'J' and resid 66 through 68 removed outlier: 3.583A pdb=" N TYR J 67 " --> pdb=" O VAL J 76 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 83 through 87 removed outlier: 6.852A pdb=" N TYR K 110 " --> pdb=" O ILE K 84 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR K 86 " --> pdb=" O TYR K 110 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE K 112 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL K 143 " --> pdb=" O ALA K 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'M' and resid 5 through 7 removed outlier: 3.731A pdb=" N VAL M 10 " --> pdb=" O THR M 7 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 42 through 46 removed outlier: 6.667A pdb=" N GLY N 97 " --> pdb=" O THR N 43 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N LEU N 45 " --> pdb=" O GLY N 97 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL N 99 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS N 127 " --> pdb=" O LEU N 100 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N LEU N 102 " --> pdb=" O LYS N 127 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL N 129 " --> pdb=" O LEU N 102 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'O' and resid 59 through 62 removed outlier: 3.721A pdb=" N TYR O 47 " --> pdb=" O ARG O 44 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP O 42 " --> pdb=" O GLN O 49 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'P' and resid 257 through 259 Processing sheet with id= N, first strand: chain 'Q' and resid 38 through 40 Processing sheet with id= O, first strand: chain 'S' and resid 50 through 52 removed outlier: 6.807A pdb=" N ALA S 76 " --> pdb=" O GLN S 68 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE S 70 " --> pdb=" O LYS S 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) 1429 hydrogen bonds defined for protein. 4074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.97 Time building geometry restraints manager: 13.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.35: 10376 1.35 - 1.58: 24014 1.58 - 1.81: 287 1.81 - 2.05: 1 2.05 - 2.28: 39 Bond restraints: 34717 Sorted by residual: bond pdb=" N PRO F 376 " pdb=" CA PRO F 376 " ideal model delta sigma weight residual 1.469 1.695 -0.227 1.28e-02 6.10e+03 3.13e+02 bond pdb=" N PRO F 444 " pdb=" CA PRO F 444 " ideal model delta sigma weight residual 1.469 1.693 -0.224 1.28e-02 6.10e+03 3.07e+02 bond pdb=" N PRO D 367 " pdb=" CA PRO D 367 " ideal model delta sigma weight residual 1.469 1.657 -0.188 1.28e-02 6.10e+03 2.16e+02 bond pdb=" C6 SQD L 402 " pdb=" S SQD L 402 " ideal model delta sigma weight residual 1.840 1.568 0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" C LEU D 371 " pdb=" O LEU D 371 " ideal model delta sigma weight residual 1.235 1.174 0.061 4.70e-03 4.53e+04 1.69e+02 ... (remaining 34712 not shown) Histogram of bond angle deviations from ideal: 73.45 - 87.31: 46 87.31 - 101.17: 143 101.17 - 115.03: 22052 115.03 - 128.89: 24746 128.89 - 142.75: 332 Bond angle restraints: 47319 Sorted by residual: angle pdb=" NB CLA F 704 " pdb="MG CLA F 704 " pdb=" ND CLA F 704 " ideal model delta sigma weight residual 176.90 113.02 63.88 3.00e+00 1.11e-01 4.53e+02 angle pdb=" CA ALA H 73 " pdb=" C ALA H 73 " pdb=" N ALA H 74 " ideal model delta sigma weight residual 116.84 87.58 29.26 1.71e+00 3.42e-01 2.93e+02 angle pdb=" C ALA H 73 " pdb=" N ALA H 74 " pdb=" CA ALA H 74 " ideal model delta sigma weight residual 121.54 91.11 30.43 1.91e+00 2.74e-01 2.54e+02 angle pdb=" C ASN D 366 " pdb=" N PRO D 367 " pdb=" CA PRO D 367 " ideal model delta sigma weight residual 119.84 138.94 -19.10 1.25e+00 6.40e-01 2.34e+02 angle pdb=" C ARG F 375 " pdb=" N PRO F 376 " pdb=" CA PRO F 376 " ideal model delta sigma weight residual 119.84 138.85 -19.01 1.25e+00 6.40e-01 2.31e+02 ... (remaining 47314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.44: 19520 30.44 - 60.88: 816 60.88 - 91.32: 50 91.32 - 121.76: 18 121.76 - 152.20: 5 Dihedral angle restraints: 20409 sinusoidal: 8067 harmonic: 12342 Sorted by residual: dihedral pdb=" CA ILE F 252 " pdb=" C ILE F 252 " pdb=" N PRO F 253 " pdb=" CA PRO F 253 " ideal model delta harmonic sigma weight residual 180.00 117.56 62.44 0 5.00e+00 4.00e-02 1.56e+02 dihedral pdb=" CA PRO B 387 " pdb=" C PRO B 387 " pdb=" N PRO B 388 " pdb=" CA PRO B 388 " ideal model delta harmonic sigma weight residual -180.00 -120.25 -59.75 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA CYS K 148 " pdb=" C CYS K 148 " pdb=" N PRO K 149 " pdb=" CA PRO K 149 " ideal model delta harmonic sigma weight residual -180.00 -126.24 -53.76 0 5.00e+00 4.00e-02 1.16e+02 ... (remaining 20406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.779: 5479 0.779 - 1.558: 0 1.558 - 2.337: 0 2.337 - 3.117: 0 3.117 - 3.896: 1 Chirality restraints: 5480 Sorted by residual: chirality pdb=" CA PRO F 36 " pdb=" N PRO F 36 " pdb=" C PRO F 36 " pdb=" CB PRO F 36 " both_signs ideal model delta sigma weight residual False 2.72 -1.18 3.90 2.00e-01 2.50e+01 3.79e+02 chirality pdb=" CA GLU C 20 " pdb=" N GLU C 20 " pdb=" C GLU C 20 " pdb=" CB GLU C 20 " both_signs ideal model delta sigma weight residual False 2.51 3.04 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CA PRO D 372 " pdb=" N PRO D 372 " pdb=" C PRO D 372 " pdb=" CB PRO D 372 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 5477 not shown) Planarity restraints: 5846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB CLA F 704 " -0.362 2.00e-02 2.50e+03 4.16e-01 2.16e+03 pdb=" ND CLA F 704 " -0.364 2.00e-02 2.50e+03 pdb=" NA CLA F 704 " -0.034 2.00e-02 2.50e+03 pdb=" NC CLA F 704 " -0.015 2.00e-02 2.50e+03 pdb="MG CLA F 704 " 0.774 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C CLA F 704 " 0.156 2.00e-02 2.50e+03 3.75e-01 1.76e+03 pdb=" C2C CLA F 704 " -0.274 2.00e-02 2.50e+03 pdb=" C4B CLA F 704 " -0.502 2.00e-02 2.50e+03 pdb=" CHC CLA F 704 " 0.593 2.00e-02 2.50e+03 pdb=" NC CLA F 704 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA F 704 " 0.024 2.00e-02 2.50e+03 2.79e-01 1.16e+03 pdb=" C2A CLA F 704 " 0.413 2.00e-02 2.50e+03 pdb=" C4A CLA F 704 " -0.347 2.00e-02 2.50e+03 pdb=" CHA CLA F 704 " -0.295 2.00e-02 2.50e+03 pdb=" NA CLA F 704 " -0.079 2.00e-02 2.50e+03 pdb="MG CLA F 704 " 0.284 2.00e-02 2.50e+03 ... (remaining 5843 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 5 2.02 - 2.74: 4248 2.74 - 3.46: 49610 3.46 - 4.18: 82728 4.18 - 4.90: 152349 Nonbonded interactions: 288940 Sorted by model distance: nonbonded pdb=" O PHE A 301 " pdb=" N GLN A 303 " model vdw 1.299 2.520 nonbonded pdb=" O4D DGD A 501 " pdb=" O2D DGD L 401 " model vdw 1.667 2.440 nonbonded pdb=" NH1 ARG F 448 " pdb=" OD1 ASP P 158 " model vdw 1.761 2.520 nonbonded pdb=" O PHE A 301 " pdb=" C LEU A 302 " model vdw 1.906 3.270 nonbonded pdb=" CEB DGD A 501 " pdb=" CHA DGD L 401 " model vdw 1.920 3.840 ... (remaining 288935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.460 Check model and map are aligned: 0.520 Set scattering table: 0.290 Process input model: 91.120 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.272 34717 Z= 0.650 Angle : 1.245 63.876 47319 Z= 0.639 Chirality : 0.075 3.896 5480 Planarity : 0.014 0.416 5846 Dihedral : 16.453 152.199 12501 Min Nonbonded Distance : 1.299 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.38 % Favored : 87.98 % Rotamer: Outliers : 1.46 % Allowed : 9.24 % Favored : 89.30 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.11), residues: 4234 helix: -1.80 (0.09), residues: 2388 sheet: -3.59 (0.33), residues: 180 loop : -3.84 (0.13), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 482 HIS 0.006 0.001 HIS P 255 PHE 0.036 0.002 PHE K 67 TYR 0.031 0.002 TYR J 60 ARG 0.042 0.001 ARG P 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 964 time to evaluate : 3.748 Fit side-chains revert: symmetry clash REVERT: A 87 GLU cc_start: 0.8372 (tt0) cc_final: 0.8089 (tt0) REVERT: A 93 ASN cc_start: 0.8436 (m-40) cc_final: 0.7662 (t0) REVERT: A 252 MET cc_start: 0.8020 (tpt) cc_final: 0.7684 (tpt) REVERT: B 100 ARG cc_start: 0.7390 (mmt180) cc_final: 0.7178 (mmt180) REVERT: B 136 PHE cc_start: 0.7766 (t80) cc_final: 0.7486 (t80) REVERT: B 178 LEU cc_start: 0.9144 (tp) cc_final: 0.8873 (mt) REVERT: B 422 ILE cc_start: 0.9081 (mt) cc_final: 0.8660 (tp) REVERT: B 427 ARG cc_start: 0.8475 (ttm170) cc_final: 0.8250 (ttp-170) REVERT: B 431 MET cc_start: 0.8430 (mmt) cc_final: 0.7655 (mmt) REVERT: B 438 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7749 (tm-30) REVERT: B 440 MET cc_start: 0.8782 (mtt) cc_final: 0.8540 (mtm) REVERT: B 466 MET cc_start: 0.7478 (mtm) cc_final: 0.7278 (mtm) REVERT: C 50 MET cc_start: 0.8598 (tpp) cc_final: 0.8382 (tpp) REVERT: C 125 ARG cc_start: 0.7353 (tpt-90) cc_final: 0.6899 (tpt170) REVERT: D 17 LEU cc_start: 0.9117 (mt) cc_final: 0.8646 (mt) REVERT: D 25 MET cc_start: 0.8804 (mmp) cc_final: 0.8515 (mmm) REVERT: D 325 MET cc_start: 0.8010 (mmm) cc_final: 0.7672 (mmm) REVERT: D 484 GLN cc_start: 0.8236 (tt0) cc_final: 0.8019 (tt0) REVERT: E 1 MET cc_start: 0.8604 (tpt) cc_final: 0.7484 (tpt) REVERT: E 86 ARG cc_start: 0.8158 (tmm-80) cc_final: 0.7827 (ttt90) REVERT: F 17 LEU cc_start: 0.8626 (mm) cc_final: 0.8286 (mt) REVERT: F 32 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8577 (mtp85) REVERT: F 238 PHE cc_start: 0.8753 (t80) cc_final: 0.8391 (t80) REVERT: F 319 TYR cc_start: 0.8234 (m-80) cc_final: 0.7812 (m-80) REVERT: F 443 LYS cc_start: 0.8923 (mttp) cc_final: 0.8425 (mttp) REVERT: F 451 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5937 (tt0) REVERT: F 487 LEU cc_start: 0.6657 (mp) cc_final: 0.6352 (tt) REVERT: F 548 MET cc_start: 0.7305 (tpp) cc_final: 0.7061 (tpp) REVERT: G 115 ILE cc_start: 0.9353 (mt) cc_final: 0.9137 (mt) REVERT: H 72 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6048 (m-10) REVERT: H 87 GLU cc_start: 0.7202 (tt0) cc_final: 0.6954 (tt0) REVERT: H 113 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8543 (t0) REVERT: H 278 GLN cc_start: 0.8336 (tt0) cc_final: 0.8114 (tt0) REVERT: H 310 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8483 (mm-40) REVERT: I 20 TYR cc_start: 0.7647 (m-80) cc_final: 0.6883 (m-80) REVERT: I 45 LYS cc_start: 0.9080 (mttt) cc_final: 0.8866 (mtpt) REVERT: I 147 LYS cc_start: 0.9061 (tptt) cc_final: 0.8679 (tppt) REVERT: J 23 ASN cc_start: 0.6700 (OUTLIER) cc_final: 0.6216 (t0) REVERT: J 87 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8294 (t0) REVERT: K 26 ILE cc_start: 0.8482 (mp) cc_final: 0.8268 (tp) REVERT: K 32 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8497 (t0) REVERT: K 110 TYR cc_start: 0.8000 (m-80) cc_final: 0.7664 (m-80) REVERT: K 200 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8001 (mm-40) REVERT: L 59 LEU cc_start: 0.9007 (mt) cc_final: 0.8732 (mt) REVERT: N 40 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8582 (mmmt) REVERT: N 86 TYR cc_start: 0.9334 (t80) cc_final: 0.8941 (t80) REVERT: N 115 TYR cc_start: 0.8759 (t80) cc_final: 0.8505 (t80) REVERT: N 135 ASP cc_start: 0.8240 (t0) cc_final: 0.7753 (t0) REVERT: N 146 TRP cc_start: 0.7744 (t-100) cc_final: 0.6411 (t-100) REVERT: P 124 MET cc_start: 0.8673 (mtm) cc_final: 0.8447 (mtp) REVERT: P 179 LYS cc_start: 0.8556 (ptmm) cc_final: 0.8334 (ptmt) REVERT: P 248 ILE cc_start: 0.8525 (mm) cc_final: 0.8169 (mm) REVERT: Q 60 ASN cc_start: 0.8594 (m-40) cc_final: 0.8309 (m-40) REVERT: Q 87 ILE cc_start: 0.8642 (tt) cc_final: 0.8419 (mm) REVERT: Q 96 ILE cc_start: 0.8442 (mt) cc_final: 0.8139 (mt) REVERT: Q 116 ILE cc_start: 0.8321 (mt) cc_final: 0.8098 (mm) REVERT: Q 142 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7327 (mt-10) REVERT: S 61 TYR cc_start: 0.8749 (t80) cc_final: 0.8049 (t80) REVERT: S 91 GLN cc_start: 0.9023 (mm110) cc_final: 0.8666 (mm-40) outliers start: 51 outliers final: 22 residues processed: 999 average time/residue: 0.4773 time to fit residues: 755.8119 Evaluate side-chains 845 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 816 time to evaluate : 3.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 446 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 456 MET Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 458 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain K residue 32 ASN Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 184 MET Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 194 LEU Chi-restraints excluded: chain Q residue 108 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 353 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 328 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 199 optimal weight: 9.9990 chunk 244 optimal weight: 0.0980 chunk 380 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 212 GLN A 355 ASN ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 GLN G 8 GLN H 14 ASN H 19 HIS H 364 GLN ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 104 GLN K 168 ASN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 355 HIS S 62 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 34717 Z= 0.242 Angle : 0.801 32.903 47319 Z= 0.373 Chirality : 0.045 0.754 5480 Planarity : 0.006 0.191 5846 Dihedral : 12.232 142.196 5134 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.57 % Favored : 90.13 % Rotamer: Outliers : 3.24 % Allowed : 15.78 % Favored : 80.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.12), residues: 4234 helix: -0.49 (0.10), residues: 2405 sheet: -3.26 (0.33), residues: 202 loop : -3.41 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 482 HIS 0.007 0.001 HIS K 181 PHE 0.025 0.001 PHE Q 36 TYR 0.032 0.001 TYR L 13 ARG 0.008 0.000 ARG F 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 876 time to evaluate : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8363 (m-40) cc_final: 0.7692 (t0) REVERT: A 157 TYR cc_start: 0.5694 (t80) cc_final: 0.5033 (t80) REVERT: A 168 GLN cc_start: 0.8614 (tt0) cc_final: 0.8392 (tt0) REVERT: A 252 MET cc_start: 0.8019 (tpt) cc_final: 0.7638 (tpt) REVERT: A 301 PHE cc_start: 0.8452 (m-10) cc_final: 0.8218 (m-80) REVERT: A 313 MET cc_start: 0.8897 (tpp) cc_final: 0.8693 (mmm) REVERT: B 167 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8825 (tp) REVERT: B 178 LEU cc_start: 0.9089 (tp) cc_final: 0.8833 (mt) REVERT: B 422 ILE cc_start: 0.9000 (mt) cc_final: 0.8615 (tp) REVERT: B 431 MET cc_start: 0.8301 (mmt) cc_final: 0.7625 (mmt) REVERT: B 438 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7711 (tm-30) REVERT: B 440 MET cc_start: 0.8716 (mtt) cc_final: 0.8496 (mtm) REVERT: B 466 MET cc_start: 0.7430 (mtm) cc_final: 0.7205 (mtm) REVERT: C 35 LEU cc_start: 0.8699 (tp) cc_final: 0.8418 (tp) REVERT: C 125 ARG cc_start: 0.7430 (tpt-90) cc_final: 0.7135 (tpt170) REVERT: D 17 LEU cc_start: 0.9056 (mt) cc_final: 0.8588 (mt) REVERT: D 325 MET cc_start: 0.8030 (mmm) cc_final: 0.7731 (mmm) REVERT: E 1 MET cc_start: 0.8551 (tpt) cc_final: 0.7388 (tpt) REVERT: E 86 ARG cc_start: 0.8105 (tmm-80) cc_final: 0.7813 (ttt-90) REVERT: F 17 LEU cc_start: 0.8531 (mm) cc_final: 0.8105 (mp) REVERT: F 96 MET cc_start: 0.7744 (mtp) cc_final: 0.7460 (mtp) REVERT: F 319 TYR cc_start: 0.8211 (m-80) cc_final: 0.7721 (m-80) REVERT: F 443 LYS cc_start: 0.9078 (mttp) cc_final: 0.8708 (mttt) REVERT: F 487 LEU cc_start: 0.6722 (mp) cc_final: 0.6377 (tt) REVERT: G 156 MET cc_start: 0.4564 (ptp) cc_final: 0.3896 (ptp) REVERT: H 29 MET cc_start: 0.8104 (mtp) cc_final: 0.7781 (mtp) REVERT: H 72 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.5557 (m-80) REVERT: H 292 GLU cc_start: 0.8313 (tp30) cc_final: 0.8039 (tp30) REVERT: H 326 GLU cc_start: 0.7389 (pm20) cc_final: 0.7107 (pt0) REVERT: I 20 TYR cc_start: 0.7560 (m-80) cc_final: 0.6835 (m-80) REVERT: I 45 LYS cc_start: 0.9033 (mttt) cc_final: 0.8793 (mtpt) REVERT: I 84 PHE cc_start: 0.8583 (t80) cc_final: 0.8228 (t80) REVERT: I 133 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7290 (mt-10) REVERT: J 23 ASN cc_start: 0.6670 (OUTLIER) cc_final: 0.6120 (t0) REVERT: J 87 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8237 (t0) REVERT: K 32 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8329 (t0) REVERT: K 66 ASP cc_start: 0.8761 (p0) cc_final: 0.8543 (p0) REVERT: K 110 TYR cc_start: 0.7919 (m-80) cc_final: 0.7706 (m-80) REVERT: K 172 ASN cc_start: 0.8141 (t0) cc_final: 0.7823 (t0) REVERT: K 200 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7962 (mm-40) REVERT: L 59 LEU cc_start: 0.9093 (mt) cc_final: 0.8855 (mt) REVERT: N 40 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8553 (mmmt) REVERT: N 86 TYR cc_start: 0.9263 (t80) cc_final: 0.8743 (t80) REVERT: N 135 ASP cc_start: 0.8318 (t0) cc_final: 0.7850 (t0) REVERT: O 37 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7740 (mtp-110) REVERT: O 49 GLN cc_start: 0.8800 (tt0) cc_final: 0.8555 (tt0) REVERT: P 124 MET cc_start: 0.8556 (mtm) cc_final: 0.8312 (mtp) REVERT: P 184 MET cc_start: 0.9211 (mmt) cc_final: 0.8814 (mmt) REVERT: P 248 ILE cc_start: 0.8371 (mm) cc_final: 0.8034 (mm) REVERT: P 340 MET cc_start: 0.8462 (ttm) cc_final: 0.8212 (ttp) REVERT: Q 28 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7070 (tm-30) REVERT: Q 60 ASN cc_start: 0.8536 (m-40) cc_final: 0.8282 (m-40) REVERT: Q 120 ASN cc_start: 0.6894 (p0) cc_final: 0.6603 (p0) REVERT: S 61 TYR cc_start: 0.8484 (t80) cc_final: 0.8132 (t80) outliers start: 113 outliers final: 73 residues processed: 939 average time/residue: 0.4544 time to fit residues: 692.8620 Evaluate side-chains 894 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 816 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 418 VAL Chi-restraints excluded: chain F residue 446 THR Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 32 ASN Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 310 ASP Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 437 LEU Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain S residue 78 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 211 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 316 optimal weight: 0.2980 chunk 259 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 381 optimal weight: 0.4980 chunk 411 optimal weight: 0.9990 chunk 339 optimal weight: 0.9990 chunk 378 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 305 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 ASN ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN H 267 GLN ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 GLN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 104 GLN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 34717 Z= 0.209 Angle : 0.754 34.590 47319 Z= 0.351 Chirality : 0.044 0.583 5480 Planarity : 0.006 0.179 5846 Dihedral : 11.357 132.569 5101 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.05 % Favored : 90.62 % Rotamer: Outliers : 3.87 % Allowed : 17.47 % Favored : 78.66 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.13), residues: 4234 helix: 0.12 (0.11), residues: 2394 sheet: -3.06 (0.33), residues: 200 loop : -3.21 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 482 HIS 0.005 0.001 HIS M 9 PHE 0.026 0.001 PHE K 67 TYR 0.028 0.001 TYR L 13 ARG 0.006 0.000 ARG F 578 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 835 time to evaluate : 3.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8329 (m-40) cc_final: 0.7724 (t0) REVERT: A 157 TYR cc_start: 0.5588 (t80) cc_final: 0.4936 (t80) REVERT: A 252 MET cc_start: 0.8053 (tpt) cc_final: 0.7729 (tpt) REVERT: A 313 MET cc_start: 0.8948 (tpp) cc_final: 0.8726 (mmm) REVERT: B 167 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8698 (tp) REVERT: B 361 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7762 (mm-30) REVERT: B 438 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7799 (tm-30) REVERT: B 440 MET cc_start: 0.8677 (mtt) cc_final: 0.8463 (mtm) REVERT: B 468 VAL cc_start: 0.8475 (t) cc_final: 0.8211 (t) REVERT: C 72 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8683 (t) REVERT: C 125 ARG cc_start: 0.7426 (tpt-90) cc_final: 0.7119 (tpt170) REVERT: D 17 LEU cc_start: 0.9070 (mt) cc_final: 0.8587 (mt) REVERT: D 366 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8279 (p0) REVERT: E 1 MET cc_start: 0.8565 (tpt) cc_final: 0.7457 (tpt) REVERT: F 319 TYR cc_start: 0.8095 (m-80) cc_final: 0.7722 (m-80) REVERT: F 443 LYS cc_start: 0.8982 (mttp) cc_final: 0.8583 (mttt) REVERT: F 466 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7916 (mp) REVERT: F 487 LEU cc_start: 0.6783 (mp) cc_final: 0.6443 (tt) REVERT: F 560 PHE cc_start: 0.7757 (m-80) cc_final: 0.7512 (m-80) REVERT: G 6 LEU cc_start: 0.9325 (tp) cc_final: 0.9088 (tt) REVERT: G 156 MET cc_start: 0.4324 (ptp) cc_final: 0.3687 (ptp) REVERT: H 29 MET cc_start: 0.7929 (mtp) cc_final: 0.7663 (mtp) REVERT: H 72 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.5439 (m-80) REVERT: H 309 TYR cc_start: 0.8932 (m-80) cc_final: 0.8501 (m-10) REVERT: H 326 GLU cc_start: 0.7282 (pm20) cc_final: 0.7082 (pt0) REVERT: I 20 TYR cc_start: 0.7648 (m-80) cc_final: 0.6980 (m-80) REVERT: I 45 LYS cc_start: 0.9020 (mttt) cc_final: 0.8757 (mtpt) REVERT: I 84 PHE cc_start: 0.8479 (t80) cc_final: 0.8130 (t80) REVERT: I 133 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7177 (mt-10) REVERT: I 139 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8982 (m) REVERT: J 22 GLN cc_start: 0.8208 (mp10) cc_final: 0.7938 (mp10) REVERT: J 23 ASN cc_start: 0.6685 (OUTLIER) cc_final: 0.6153 (t0) REVERT: J 87 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8209 (t0) REVERT: K 66 ASP cc_start: 0.8813 (p0) cc_final: 0.8547 (p0) REVERT: K 110 TYR cc_start: 0.7862 (m-80) cc_final: 0.7656 (m-80) REVERT: M 19 ASP cc_start: 0.7394 (p0) cc_final: 0.6533 (t0) REVERT: M 72 ARG cc_start: 0.8725 (mtt-85) cc_final: 0.8493 (mtt-85) REVERT: N 40 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8540 (mmmt) REVERT: N 86 TYR cc_start: 0.9259 (t80) cc_final: 0.8773 (t80) REVERT: N 135 ASP cc_start: 0.8367 (t0) cc_final: 0.7894 (t0) REVERT: P 124 MET cc_start: 0.8564 (mtm) cc_final: 0.8296 (mtp) REVERT: P 248 ILE cc_start: 0.8297 (mm) cc_final: 0.7910 (mm) REVERT: P 310 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.8001 (p0) REVERT: P 340 MET cc_start: 0.8282 (ttm) cc_final: 0.8073 (ttp) REVERT: P 428 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8179 (tt) REVERT: Q 60 ASN cc_start: 0.8503 (m-40) cc_final: 0.8299 (m-40) REVERT: Q 83 LYS cc_start: 0.8454 (tttp) cc_final: 0.7655 (tppt) REVERT: S 61 TYR cc_start: 0.8613 (t80) cc_final: 0.8038 (t80) outliers start: 135 outliers final: 96 residues processed: 915 average time/residue: 0.4741 time to fit residues: 709.3793 Evaluate side-chains 885 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 779 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 65 PHE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 310 ASP Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 428 ILE Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 376 optimal weight: 0.8980 chunk 286 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 255 optimal weight: 0.3980 chunk 382 optimal weight: 0.6980 chunk 405 optimal weight: 2.9990 chunk 199 optimal weight: 0.0670 chunk 362 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 166 GLN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 267 GLN ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 104 GLN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN M 95 ASN Q 108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 34717 Z= 0.188 Angle : 0.665 16.306 47319 Z= 0.323 Chirality : 0.043 0.529 5480 Planarity : 0.005 0.163 5846 Dihedral : 10.638 127.108 5094 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.88 % Favored : 90.81 % Rotamer: Outliers : 4.42 % Allowed : 18.93 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 4234 helix: 0.44 (0.11), residues: 2385 sheet: -2.96 (0.35), residues: 190 loop : -3.09 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 280 HIS 0.005 0.001 HIS M 9 PHE 0.023 0.001 PHE K 67 TYR 0.026 0.001 TYR L 13 ARG 0.007 0.000 ARG F 578 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 819 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8281 (m-40) cc_final: 0.7750 (t0) REVERT: A 157 TYR cc_start: 0.5586 (t80) cc_final: 0.4917 (t80) REVERT: A 252 MET cc_start: 0.8065 (tpt) cc_final: 0.7764 (tpt) REVERT: A 271 LEU cc_start: 0.8053 (mt) cc_final: 0.7823 (mm) REVERT: A 313 MET cc_start: 0.8947 (tpp) cc_final: 0.8720 (mmm) REVERT: B 167 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8630 (tp) REVERT: B 361 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7712 (mm-30) REVERT: B 438 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7768 (tm-30) REVERT: B 468 VAL cc_start: 0.8391 (t) cc_final: 0.8100 (t) REVERT: C 70 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.5862 (p90) REVERT: C 72 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8656 (t) REVERT: C 125 ARG cc_start: 0.7441 (tpt-90) cc_final: 0.7143 (tpt170) REVERT: D 76 LEU cc_start: 0.9112 (tp) cc_final: 0.8897 (tp) REVERT: E 1 MET cc_start: 0.8588 (tpt) cc_final: 0.7512 (tpt) REVERT: E 19 TYR cc_start: 0.9044 (t80) cc_final: 0.8775 (t80) REVERT: E 86 ARG cc_start: 0.7567 (ttp80) cc_final: 0.7268 (ttp80) REVERT: F 17 LEU cc_start: 0.8492 (mm) cc_final: 0.8217 (mt) REVERT: F 179 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9050 (p) REVERT: F 319 TYR cc_start: 0.8101 (m-80) cc_final: 0.7715 (m-80) REVERT: F 466 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7902 (mp) REVERT: F 487 LEU cc_start: 0.6770 (mp) cc_final: 0.6443 (tt) REVERT: G 156 MET cc_start: 0.4304 (ptp) cc_final: 0.3808 (ptp) REVERT: H 8 THR cc_start: 0.8773 (t) cc_final: 0.8486 (p) REVERT: H 29 MET cc_start: 0.7959 (mtp) cc_final: 0.7729 (mtp) REVERT: H 94 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.9037 (t) REVERT: H 267 GLN cc_start: 0.8029 (mt0) cc_final: 0.7807 (mt0) REVERT: H 309 TYR cc_start: 0.8944 (m-80) cc_final: 0.8526 (m-10) REVERT: H 326 GLU cc_start: 0.7339 (pm20) cc_final: 0.7136 (pt0) REVERT: H 373 MET cc_start: 0.6278 (mmt) cc_final: 0.6061 (mmt) REVERT: I 20 TYR cc_start: 0.7573 (m-80) cc_final: 0.6948 (m-80) REVERT: I 53 ARG cc_start: 0.9089 (mtm-85) cc_final: 0.8788 (mtm-85) REVERT: I 84 PHE cc_start: 0.8499 (t80) cc_final: 0.8152 (t80) REVERT: I 133 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7218 (mt-10) REVERT: I 139 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8965 (m) REVERT: J 22 GLN cc_start: 0.8285 (mp10) cc_final: 0.8005 (mp10) REVERT: J 23 ASN cc_start: 0.6680 (OUTLIER) cc_final: 0.6138 (t0) REVERT: J 87 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8142 (t0) REVERT: L 29 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: M 19 ASP cc_start: 0.7097 (p0) cc_final: 0.6259 (t0) REVERT: M 52 LYS cc_start: 0.8863 (tppt) cc_final: 0.8609 (tptt) REVERT: N 40 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8504 (mmmt) REVERT: N 86 TYR cc_start: 0.9192 (t80) cc_final: 0.8806 (t80) REVERT: N 123 LEU cc_start: 0.7598 (tp) cc_final: 0.7366 (tp) REVERT: O 61 LEU cc_start: 0.8707 (mt) cc_final: 0.8445 (mt) REVERT: P 124 MET cc_start: 0.8529 (mtm) cc_final: 0.8247 (mtp) REVERT: P 138 MET cc_start: 0.8452 (tpt) cc_final: 0.7999 (tpt) REVERT: Q 28 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7158 (tm-30) REVERT: Q 60 ASN cc_start: 0.8500 (m-40) cc_final: 0.8295 (m-40) REVERT: Q 83 LYS cc_start: 0.8508 (tttp) cc_final: 0.7701 (tppt) REVERT: Q 132 MET cc_start: 0.8264 (mpp) cc_final: 0.8051 (mpp) REVERT: S 61 TYR cc_start: 0.8598 (t80) cc_final: 0.8043 (t80) outliers start: 154 outliers final: 101 residues processed: 913 average time/residue: 0.4706 time to fit residues: 705.5836 Evaluate side-chains 888 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 777 time to evaluate : 3.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 587 SER Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain S residue 78 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 337 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 301 optimal weight: 6.9990 chunk 167 optimal weight: 0.9990 chunk 345 optimal weight: 0.9990 chunk 279 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 363 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 104 GLN K 168 ASN ** K 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 34717 Z= 0.213 Angle : 0.662 13.808 47319 Z= 0.323 Chirality : 0.043 0.505 5480 Planarity : 0.005 0.152 5846 Dihedral : 10.330 124.995 5092 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.14 % Favored : 90.62 % Rotamer: Outliers : 4.59 % Allowed : 19.76 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 4234 helix: 0.63 (0.11), residues: 2368 sheet: -2.71 (0.36), residues: 180 loop : -2.99 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 482 HIS 0.007 0.001 HIS K 181 PHE 0.027 0.001 PHE K 67 TYR 0.027 0.001 TYR L 13 ARG 0.009 0.000 ARG F 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 784 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8985 (mmt) cc_final: 0.8656 (mmm) REVERT: A 93 ASN cc_start: 0.8261 (m-40) cc_final: 0.7748 (t0) REVERT: A 157 TYR cc_start: 0.5576 (t80) cc_final: 0.4923 (t80) REVERT: A 252 MET cc_start: 0.8125 (tpt) cc_final: 0.7803 (tpt) REVERT: A 271 LEU cc_start: 0.8067 (mt) cc_final: 0.7856 (mm) REVERT: A 313 MET cc_start: 0.8928 (tpp) cc_final: 0.8701 (mmm) REVERT: B 136 PHE cc_start: 0.7754 (t80) cc_final: 0.7457 (t80) REVERT: B 140 GLU cc_start: 0.2569 (OUTLIER) cc_final: 0.2244 (pt0) REVERT: B 167 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8498 (tp) REVERT: B 361 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 438 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7792 (tm-30) REVERT: B 468 VAL cc_start: 0.8323 (t) cc_final: 0.8015 (t) REVERT: C 70 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.5907 (p90) REVERT: C 72 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8633 (t) REVERT: C 125 ARG cc_start: 0.7463 (tpt-90) cc_final: 0.7176 (tpt170) REVERT: D 17 LEU cc_start: 0.9043 (mt) cc_final: 0.8593 (mt) REVERT: E 1 MET cc_start: 0.8602 (tpt) cc_final: 0.7535 (tpt) REVERT: E 19 TYR cc_start: 0.9047 (t80) cc_final: 0.8803 (t80) REVERT: F 17 LEU cc_start: 0.8509 (mm) cc_final: 0.8195 (mt) REVERT: F 319 TYR cc_start: 0.8029 (m-80) cc_final: 0.7616 (m-80) REVERT: F 466 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7908 (mp) REVERT: F 487 LEU cc_start: 0.6753 (mp) cc_final: 0.6468 (tt) REVERT: G 156 MET cc_start: 0.4301 (ptp) cc_final: 0.3825 (ptp) REVERT: H 8 THR cc_start: 0.8783 (t) cc_final: 0.8537 (p) REVERT: H 29 MET cc_start: 0.7969 (mtp) cc_final: 0.7751 (mtp) REVERT: H 267 GLN cc_start: 0.8061 (mt0) cc_final: 0.7809 (mt0) REVERT: H 292 GLU cc_start: 0.8292 (tp30) cc_final: 0.7820 (mm-30) REVERT: H 309 TYR cc_start: 0.8945 (m-80) cc_final: 0.8555 (m-10) REVERT: I 20 TYR cc_start: 0.7514 (m-80) cc_final: 0.6939 (m-80) REVERT: I 45 LYS cc_start: 0.9163 (mtpp) cc_final: 0.8899 (mtpt) REVERT: I 84 PHE cc_start: 0.8585 (t80) cc_final: 0.8270 (t80) REVERT: I 133 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7188 (mt-10) REVERT: I 139 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8959 (m) REVERT: J 22 GLN cc_start: 0.8312 (mp10) cc_final: 0.8105 (mp10) REVERT: J 23 ASN cc_start: 0.6572 (OUTLIER) cc_final: 0.5988 (t0) REVERT: J 87 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8198 (t0) REVERT: J 168 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.5495 (p90) REVERT: K 66 ASP cc_start: 0.8842 (p0) cc_final: 0.8506 (p0) REVERT: L 29 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: N 40 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8674 (mmmt) REVERT: N 86 TYR cc_start: 0.9271 (t80) cc_final: 0.8780 (t80) REVERT: N 123 LEU cc_start: 0.7596 (tp) cc_final: 0.7391 (tp) REVERT: N 146 TRP cc_start: 0.8840 (t60) cc_final: 0.8604 (t60) REVERT: P 124 MET cc_start: 0.8551 (mtm) cc_final: 0.8239 (mtp) REVERT: P 138 MET cc_start: 0.8415 (tpt) cc_final: 0.8000 (tpt) REVERT: Q 28 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7243 (tm-30) REVERT: Q 60 ASN cc_start: 0.8503 (m-40) cc_final: 0.8297 (m-40) REVERT: Q 83 LYS cc_start: 0.8515 (tttp) cc_final: 0.7711 (tppt) REVERT: S 61 TYR cc_start: 0.8599 (t80) cc_final: 0.8020 (t80) outliers start: 160 outliers final: 123 residues processed: 885 average time/residue: 0.4451 time to fit residues: 642.3049 Evaluate side-chains 899 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 766 time to evaluate : 3.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 560 PHE Chi-restraints excluded: chain F residue 587 SER Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 65 PHE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 136 optimal weight: 3.9990 chunk 364 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 99 optimal weight: 0.0060 chunk 405 optimal weight: 2.9990 chunk 336 optimal weight: 4.9990 chunk 187 optimal weight: 0.0050 chunk 33 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 212 optimal weight: 0.9990 overall best weight: 0.5410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN I 178 GLN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 104 GLN K 172 ASN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 34717 Z= 0.186 Angle : 0.649 11.912 47319 Z= 0.316 Chirality : 0.043 0.477 5480 Planarity : 0.005 0.142 5846 Dihedral : 9.964 122.065 5092 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.00 % Favored : 90.79 % Rotamer: Outliers : 4.59 % Allowed : 19.99 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 4234 helix: 0.75 (0.11), residues: 2378 sheet: -2.63 (0.36), residues: 194 loop : -2.92 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 280 HIS 0.004 0.001 HIS M 9 PHE 0.025 0.001 PHE K 67 TYR 0.024 0.001 TYR L 13 ARG 0.010 0.000 ARG F 578 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 800 time to evaluate : 3.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8872 (mmt) cc_final: 0.8503 (mmm) REVERT: A 93 ASN cc_start: 0.8222 (m-40) cc_final: 0.7745 (t0) REVERT: A 157 TYR cc_start: 0.5610 (t80) cc_final: 0.4945 (t80) REVERT: A 252 MET cc_start: 0.8101 (tpt) cc_final: 0.7784 (tpt) REVERT: A 271 LEU cc_start: 0.8069 (mt) cc_final: 0.7852 (mm) REVERT: A 313 MET cc_start: 0.8874 (tpp) cc_final: 0.8637 (mmm) REVERT: B 136 PHE cc_start: 0.7797 (t80) cc_final: 0.7496 (t80) REVERT: B 140 GLU cc_start: 0.2490 (OUTLIER) cc_final: 0.2183 (pt0) REVERT: B 167 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8408 (tp) REVERT: B 361 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 432 MET cc_start: 0.8322 (ttm) cc_final: 0.8090 (mtp) REVERT: B 438 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7767 (tm-30) REVERT: B 468 VAL cc_start: 0.8313 (t) cc_final: 0.8078 (t) REVERT: C 70 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.6256 (p90) REVERT: C 72 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8609 (t) REVERT: C 125 ARG cc_start: 0.7467 (tpt-90) cc_final: 0.7175 (tpt170) REVERT: D 17 LEU cc_start: 0.9025 (mt) cc_final: 0.8631 (mt) REVERT: E 1 MET cc_start: 0.8584 (tpt) cc_final: 0.7519 (tpt) REVERT: E 19 TYR cc_start: 0.9014 (t80) cc_final: 0.8809 (t80) REVERT: F 17 LEU cc_start: 0.8483 (mm) cc_final: 0.8165 (mt) REVERT: F 319 TYR cc_start: 0.7986 (m-80) cc_final: 0.7484 (m-80) REVERT: F 466 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7899 (mp) REVERT: F 487 LEU cc_start: 0.6955 (mp) cc_final: 0.6580 (tt) REVERT: F 560 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.6757 (t80) REVERT: G 156 MET cc_start: 0.4265 (ptp) cc_final: 0.3817 (ptp) REVERT: H 29 MET cc_start: 0.7939 (mtp) cc_final: 0.7687 (mtp) REVERT: H 116 LEU cc_start: 0.8860 (tp) cc_final: 0.8631 (tp) REVERT: H 234 LEU cc_start: 0.9264 (mt) cc_final: 0.9045 (mp) REVERT: H 292 GLU cc_start: 0.8294 (tp30) cc_final: 0.7876 (mm-30) REVERT: H 309 TYR cc_start: 0.8953 (m-80) cc_final: 0.8565 (m-10) REVERT: H 374 LYS cc_start: 0.7446 (mmpt) cc_final: 0.6847 (mmmt) REVERT: I 20 TYR cc_start: 0.7532 (m-80) cc_final: 0.6910 (m-80) REVERT: I 53 ARG cc_start: 0.9164 (mtm-85) cc_final: 0.8919 (mtm-85) REVERT: I 84 PHE cc_start: 0.8548 (t80) cc_final: 0.8258 (t80) REVERT: I 133 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7155 (mt-10) REVERT: J 22 GLN cc_start: 0.8314 (mp10) cc_final: 0.8042 (mp10) REVERT: J 23 ASN cc_start: 0.6674 (OUTLIER) cc_final: 0.6088 (t0) REVERT: J 87 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8187 (t0) REVERT: J 168 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.5606 (p90) REVERT: K 66 ASP cc_start: 0.8819 (p0) cc_final: 0.8458 (p0) REVERT: L 29 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: N 40 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8682 (mmmt) REVERT: N 86 TYR cc_start: 0.9234 (t80) cc_final: 0.8779 (t80) REVERT: N 123 LEU cc_start: 0.7595 (tp) cc_final: 0.7389 (tp) REVERT: N 146 TRP cc_start: 0.8891 (t60) cc_final: 0.8534 (t60) REVERT: P 124 MET cc_start: 0.8543 (mtm) cc_final: 0.8223 (mtp) REVERT: P 274 MET cc_start: 0.8150 (ptp) cc_final: 0.7859 (mtm) REVERT: P 290 ARG cc_start: 0.8108 (mtt180) cc_final: 0.7881 (mtt180) REVERT: Q 83 LYS cc_start: 0.8427 (tttp) cc_final: 0.7659 (tppt) REVERT: S 61 TYR cc_start: 0.8580 (t80) cc_final: 0.8043 (t80) outliers start: 160 outliers final: 118 residues processed: 898 average time/residue: 0.4584 time to fit residues: 670.0383 Evaluate side-chains 902 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 774 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 560 PHE Chi-restraints excluded: chain F residue 562 ASP Chi-restraints excluded: chain F residue 587 SER Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 172 ASN Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 309 THR Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 80 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 390 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 296 optimal weight: 3.9990 chunk 229 optimal weight: 0.8980 chunk 341 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 403 optimal weight: 1.9990 chunk 252 optimal weight: 0.0670 chunk 246 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 198 GLN F 67 GLN F 359 ASN H 14 ASN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 267 GLN H 361 ASN ** I 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 104 GLN K 168 ASN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 365 GLN Q 31 GLN ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 34717 Z= 0.211 Angle : 0.657 11.912 47319 Z= 0.318 Chirality : 0.043 0.477 5480 Planarity : 0.005 0.133 5846 Dihedral : 9.686 121.317 5092 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.28 % Favored : 90.51 % Rotamer: Outliers : 4.93 % Allowed : 20.02 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 4234 helix: 0.83 (0.11), residues: 2372 sheet: -2.46 (0.36), residues: 190 loop : -2.88 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 280 HIS 0.004 0.001 HIS K 181 PHE 0.026 0.001 PHE K 67 TYR 0.027 0.001 TYR L 13 ARG 0.009 0.000 ARG F 578 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 777 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8254 (m-40) cc_final: 0.7788 (t0) REVERT: A 157 TYR cc_start: 0.5633 (t80) cc_final: 0.4969 (t80) REVERT: A 197 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8137 (mm-30) REVERT: A 252 MET cc_start: 0.8139 (tpt) cc_final: 0.7854 (tpt) REVERT: A 271 LEU cc_start: 0.8082 (mt) cc_final: 0.7863 (mm) REVERT: A 313 MET cc_start: 0.8874 (tpp) cc_final: 0.8649 (mmm) REVERT: B 140 GLU cc_start: 0.2524 (OUTLIER) cc_final: 0.2166 (pt0) REVERT: B 167 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8418 (tp) REVERT: B 361 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7583 (mm-30) REVERT: B 438 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7769 (tm-30) REVERT: B 468 VAL cc_start: 0.8341 (t) cc_final: 0.8096 (t) REVERT: C 70 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.6187 (p90) REVERT: C 125 ARG cc_start: 0.7463 (tpt-90) cc_final: 0.7189 (tpt170) REVERT: D 17 LEU cc_start: 0.9025 (mt) cc_final: 0.8632 (mt) REVERT: E 1 MET cc_start: 0.8589 (tpt) cc_final: 0.7533 (tpt) REVERT: F 17 LEU cc_start: 0.8471 (mm) cc_final: 0.8161 (mt) REVERT: F 319 TYR cc_start: 0.8002 (m-80) cc_final: 0.7518 (m-80) REVERT: F 464 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7053 (tp) REVERT: F 466 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7933 (mp) REVERT: F 487 LEU cc_start: 0.6911 (mp) cc_final: 0.6531 (tt) REVERT: F 560 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6767 (t80) REVERT: G 28 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8830 (mp) REVERT: H 29 MET cc_start: 0.7969 (mtp) cc_final: 0.7762 (mtp) REVERT: H 116 LEU cc_start: 0.8848 (tp) cc_final: 0.8570 (tp) REVERT: H 292 GLU cc_start: 0.8281 (tp30) cc_final: 0.7855 (mm-30) REVERT: H 309 TYR cc_start: 0.8958 (m-80) cc_final: 0.8577 (m-10) REVERT: I 20 TYR cc_start: 0.7517 (m-80) cc_final: 0.6927 (m-80) REVERT: I 84 PHE cc_start: 0.8537 (t80) cc_final: 0.8263 (t80) REVERT: I 133 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7119 (mt-10) REVERT: J 22 GLN cc_start: 0.8321 (mp10) cc_final: 0.7972 (mp10) REVERT: J 23 ASN cc_start: 0.6596 (OUTLIER) cc_final: 0.5987 (t0) REVERT: J 87 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8215 (t0) REVERT: J 168 TYR cc_start: 0.7317 (OUTLIER) cc_final: 0.5528 (p90) REVERT: K 66 ASP cc_start: 0.8857 (p0) cc_final: 0.8499 (p0) REVERT: L 29 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: L 59 LEU cc_start: 0.9093 (mt) cc_final: 0.8746 (mt) REVERT: N 40 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8681 (mmmt) REVERT: N 86 TYR cc_start: 0.9220 (t80) cc_final: 0.8833 (t80) REVERT: N 123 LEU cc_start: 0.7662 (tp) cc_final: 0.7461 (tp) REVERT: P 124 MET cc_start: 0.8511 (mtm) cc_final: 0.8166 (mtp) REVERT: P 138 MET cc_start: 0.8417 (tpt) cc_final: 0.8064 (tpt) REVERT: P 274 MET cc_start: 0.8145 (ptp) cc_final: 0.7858 (mtm) REVERT: P 381 VAL cc_start: 0.9032 (t) cc_final: 0.8659 (p) REVERT: Q 83 LYS cc_start: 0.8432 (tttp) cc_final: 0.7664 (tppt) REVERT: S 61 TYR cc_start: 0.8607 (t80) cc_final: 0.8114 (t80) outliers start: 172 outliers final: 135 residues processed: 882 average time/residue: 0.4398 time to fit residues: 634.7910 Evaluate side-chains 905 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 759 time to evaluate : 3.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 560 PHE Chi-restraints excluded: chain F residue 562 ASP Chi-restraints excluded: chain F residue 587 SER Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 65 PHE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 309 THR Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 365 GLN Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 80 GLU Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 249 optimal weight: 0.5980 chunk 161 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 256 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 317 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 ASN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 267 GLN ** I 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 104 GLN K 172 ASN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 GLN ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 34717 Z= 0.201 Angle : 0.653 14.239 47319 Z= 0.317 Chirality : 0.043 0.457 5480 Planarity : 0.005 0.127 5846 Dihedral : 9.469 119.625 5092 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.33 % Favored : 90.46 % Rotamer: Outliers : 4.85 % Allowed : 20.57 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 4234 helix: 0.91 (0.11), residues: 2370 sheet: -2.43 (0.36), residues: 193 loop : -2.85 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 280 HIS 0.004 0.001 HIS C 99 PHE 0.028 0.001 PHE P 57 TYR 0.025 0.001 TYR L 13 ARG 0.009 0.000 ARG F 578 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 767 time to evaluate : 3.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8233 (m-40) cc_final: 0.7790 (t0) REVERT: A 157 TYR cc_start: 0.5632 (t80) cc_final: 0.4972 (t80) REVERT: A 252 MET cc_start: 0.8137 (tpt) cc_final: 0.7872 (tpt) REVERT: A 271 LEU cc_start: 0.8098 (mt) cc_final: 0.7870 (mm) REVERT: A 313 MET cc_start: 0.8863 (tpp) cc_final: 0.8628 (mmm) REVERT: B 140 GLU cc_start: 0.2444 (OUTLIER) cc_final: 0.2189 (pt0) REVERT: B 167 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8399 (tp) REVERT: B 361 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7567 (mm-30) REVERT: B 438 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7725 (tm-30) REVERT: B 468 VAL cc_start: 0.8280 (t) cc_final: 0.8039 (t) REVERT: C 70 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.6246 (p90) REVERT: C 125 ARG cc_start: 0.7509 (tpt-90) cc_final: 0.7230 (tpt170) REVERT: D 17 LEU cc_start: 0.9000 (mt) cc_final: 0.8626 (mt) REVERT: D 24 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9087 (tt) REVERT: D 140 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6484 (mt-10) REVERT: E 1 MET cc_start: 0.8585 (tpt) cc_final: 0.7535 (tpt) REVERT: F 17 LEU cc_start: 0.8419 (mm) cc_final: 0.8162 (mt) REVERT: F 319 TYR cc_start: 0.7986 (m-80) cc_final: 0.7506 (m-80) REVERT: F 464 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7043 (tp) REVERT: F 466 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7810 (mp) REVERT: F 487 LEU cc_start: 0.7014 (mp) cc_final: 0.6638 (tt) REVERT: F 560 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.6773 (t80) REVERT: G 28 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8836 (mp) REVERT: H 29 MET cc_start: 0.8011 (mtp) cc_final: 0.7729 (mtp) REVERT: H 116 LEU cc_start: 0.8866 (tp) cc_final: 0.8562 (tp) REVERT: H 292 GLU cc_start: 0.8223 (tp30) cc_final: 0.7834 (mm-30) REVERT: H 309 TYR cc_start: 0.8953 (m-80) cc_final: 0.8568 (m-10) REVERT: H 374 LYS cc_start: 0.7439 (mmpt) cc_final: 0.6788 (mmmt) REVERT: I 20 TYR cc_start: 0.7482 (m-80) cc_final: 0.6906 (m-80) REVERT: I 84 PHE cc_start: 0.8493 (t80) cc_final: 0.8243 (t80) REVERT: I 133 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7118 (mt-10) REVERT: J 22 GLN cc_start: 0.8324 (mp10) cc_final: 0.8057 (mp10) REVERT: J 23 ASN cc_start: 0.6603 (OUTLIER) cc_final: 0.6003 (t0) REVERT: J 87 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8220 (t0) REVERT: J 168 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.5681 (p90) REVERT: K 47 MET cc_start: 0.8339 (tpt) cc_final: 0.8102 (tpp) REVERT: K 66 ASP cc_start: 0.8847 (p0) cc_final: 0.8459 (p0) REVERT: L 29 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8095 (m-80) REVERT: L 59 LEU cc_start: 0.9084 (mt) cc_final: 0.8743 (mt) REVERT: N 40 LYS cc_start: 0.8891 (mmtt) cc_final: 0.8683 (mmmt) REVERT: N 86 TYR cc_start: 0.9205 (t80) cc_final: 0.8819 (t80) REVERT: N 123 LEU cc_start: 0.7639 (tp) cc_final: 0.7425 (tp) REVERT: O 49 GLN cc_start: 0.8783 (tt0) cc_final: 0.8470 (tt0) REVERT: P 124 MET cc_start: 0.8520 (mtm) cc_final: 0.8158 (mtp) REVERT: P 138 MET cc_start: 0.8408 (tpt) cc_final: 0.8014 (tpt) REVERT: P 274 MET cc_start: 0.8095 (ptp) cc_final: 0.7814 (mtm) REVERT: P 381 VAL cc_start: 0.9020 (t) cc_final: 0.8654 (p) REVERT: Q 83 LYS cc_start: 0.8397 (tttp) cc_final: 0.7680 (tppt) REVERT: S 61 TYR cc_start: 0.8602 (t80) cc_final: 0.8141 (t80) outliers start: 169 outliers final: 137 residues processed: 869 average time/residue: 0.4484 time to fit residues: 636.3633 Evaluate side-chains 903 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 754 time to evaluate : 3.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 560 PHE Chi-restraints excluded: chain F residue 562 ASP Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 65 PHE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 172 ASN Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 309 THR Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 80 GLU Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 367 optimal weight: 0.9980 chunk 386 optimal weight: 2.9990 chunk 352 optimal weight: 1.9990 chunk 376 optimal weight: 0.7980 chunk 226 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 295 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 340 optimal weight: 0.8980 chunk 355 optimal weight: 0.8980 chunk 375 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 ASN K 104 GLN K 168 ASN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 HIS P 365 GLN ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 34717 Z= 0.226 Angle : 0.670 14.267 47319 Z= 0.324 Chirality : 0.043 0.444 5480 Planarity : 0.005 0.121 5846 Dihedral : 9.329 118.980 5090 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.54 % Favored : 90.27 % Rotamer: Outliers : 4.70 % Allowed : 21.11 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 4234 helix: 0.94 (0.11), residues: 2375 sheet: -2.30 (0.39), residues: 174 loop : -2.84 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 71 HIS 0.005 0.001 HIS C 99 PHE 0.038 0.001 PHE P 57 TYR 0.027 0.001 TYR L 13 ARG 0.010 0.000 ARG F 578 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 753 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8230 (m-40) cc_final: 0.7795 (t0) REVERT: A 157 TYR cc_start: 0.5665 (t80) cc_final: 0.4997 (t80) REVERT: A 252 MET cc_start: 0.8144 (tpt) cc_final: 0.7869 (tpt) REVERT: A 271 LEU cc_start: 0.8112 (mt) cc_final: 0.7882 (mm) REVERT: A 313 MET cc_start: 0.8909 (tpp) cc_final: 0.8683 (mmm) REVERT: B 140 GLU cc_start: 0.2454 (OUTLIER) cc_final: 0.2217 (pt0) REVERT: B 167 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8440 (tp) REVERT: B 361 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7566 (mm-30) REVERT: B 438 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 468 VAL cc_start: 0.8317 (t) cc_final: 0.8081 (t) REVERT: C 70 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.6263 (p90) REVERT: C 125 ARG cc_start: 0.7624 (tpt-90) cc_final: 0.7405 (tpt170) REVERT: D 17 LEU cc_start: 0.9037 (mt) cc_final: 0.8660 (mt) REVERT: D 140 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6490 (mt-10) REVERT: E 1 MET cc_start: 0.8577 (tpt) cc_final: 0.7511 (tpt) REVERT: F 58 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8721 (m) REVERT: F 319 TYR cc_start: 0.7993 (m-80) cc_final: 0.7483 (m-80) REVERT: F 464 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7050 (tp) REVERT: F 466 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7820 (mp) REVERT: F 487 LEU cc_start: 0.6945 (mp) cc_final: 0.6487 (tt) REVERT: F 560 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.6754 (t80) REVERT: G 28 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8849 (mp) REVERT: G 114 MET cc_start: 0.8877 (tmm) cc_final: 0.7808 (ttp) REVERT: H 29 MET cc_start: 0.8038 (mtp) cc_final: 0.7740 (mtp) REVERT: H 116 LEU cc_start: 0.8849 (tp) cc_final: 0.8530 (tp) REVERT: H 292 GLU cc_start: 0.8212 (tp30) cc_final: 0.7857 (mm-30) REVERT: H 309 TYR cc_start: 0.8957 (m-80) cc_final: 0.8569 (m-10) REVERT: H 335 LYS cc_start: 0.8786 (mtmm) cc_final: 0.8427 (mtmt) REVERT: I 19 LYS cc_start: 0.8113 (tppt) cc_final: 0.7884 (tppt) REVERT: I 20 TYR cc_start: 0.7471 (m-80) cc_final: 0.6898 (m-80) REVERT: I 84 PHE cc_start: 0.8498 (t80) cc_final: 0.8253 (t80) REVERT: I 133 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7135 (mt-10) REVERT: J 22 GLN cc_start: 0.8339 (mp10) cc_final: 0.8076 (mp10) REVERT: J 23 ASN cc_start: 0.6630 (OUTLIER) cc_final: 0.6031 (t0) REVERT: J 87 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8236 (t0) REVERT: J 168 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.5680 (p90) REVERT: K 47 MET cc_start: 0.8423 (tpt) cc_final: 0.8198 (tpp) REVERT: L 29 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: L 59 LEU cc_start: 0.9075 (mt) cc_final: 0.8743 (mt) REVERT: N 40 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8687 (mmmt) REVERT: N 86 TYR cc_start: 0.9211 (t80) cc_final: 0.8852 (t80) REVERT: N 123 LEU cc_start: 0.7534 (tp) cc_final: 0.7332 (tp) REVERT: O 49 GLN cc_start: 0.8770 (tt0) cc_final: 0.8455 (tt0) REVERT: P 124 MET cc_start: 0.8571 (mtm) cc_final: 0.8207 (mtp) REVERT: P 138 MET cc_start: 0.8387 (tpt) cc_final: 0.7993 (tpt) REVERT: P 248 ILE cc_start: 0.8365 (mm) cc_final: 0.8085 (mm) REVERT: P 290 ARG cc_start: 0.8181 (mtt180) cc_final: 0.7867 (mtt180) REVERT: P 381 VAL cc_start: 0.9015 (t) cc_final: 0.8662 (p) REVERT: Q 83 LYS cc_start: 0.8401 (tttp) cc_final: 0.7682 (tppt) REVERT: S 52 LYS cc_start: 0.8466 (ptmm) cc_final: 0.8253 (ptmm) REVERT: S 61 TYR cc_start: 0.8609 (t80) cc_final: 0.8132 (t80) outliers start: 164 outliers final: 141 residues processed: 852 average time/residue: 0.4495 time to fit residues: 627.1412 Evaluate side-chains 895 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 742 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 445 MET Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 560 PHE Chi-restraints excluded: chain F residue 562 ASP Chi-restraints excluded: chain F residue 587 SER Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 65 PHE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 232 THR Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 309 THR Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain P residue 435 ASN Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 80 GLU Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 247 optimal weight: 0.9980 chunk 397 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 276 optimal weight: 0.7980 chunk 417 optimal weight: 0.8980 chunk 384 optimal weight: 0.0980 chunk 332 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 256 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN D 198 GLN D 402 GLN E 87 ASN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 267 GLN ** I 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 104 GLN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN M 109 ASN ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 34717 Z= 0.194 Angle : 0.662 16.129 47319 Z= 0.318 Chirality : 0.043 0.418 5480 Planarity : 0.005 0.114 5846 Dihedral : 9.147 118.268 5090 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.31 % Favored : 90.51 % Rotamer: Outliers : 4.53 % Allowed : 21.69 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4234 helix: 1.02 (0.11), residues: 2379 sheet: -2.16 (0.40), residues: 168 loop : -2.79 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 454 HIS 0.004 0.001 HIS C 99 PHE 0.026 0.001 PHE H 131 TYR 0.025 0.001 TYR L 13 ARG 0.010 0.000 ARG F 578 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 755 time to evaluate : 3.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.5696 (t80) cc_final: 0.4995 (t80) REVERT: A 252 MET cc_start: 0.8126 (tpt) cc_final: 0.7865 (tpt) REVERT: A 271 LEU cc_start: 0.8102 (mt) cc_final: 0.7875 (mm) REVERT: A 313 MET cc_start: 0.8881 (tpp) cc_final: 0.8659 (mmm) REVERT: B 67 THR cc_start: 0.7775 (p) cc_final: 0.7573 (t) REVERT: B 140 GLU cc_start: 0.2656 (OUTLIER) cc_final: 0.1856 (pm20) REVERT: B 167 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8408 (tp) REVERT: B 361 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 438 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7729 (tm-30) REVERT: B 468 VAL cc_start: 0.8345 (t) cc_final: 0.8115 (t) REVERT: C 70 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.5921 (p90) REVERT: C 125 ARG cc_start: 0.7625 (tpt-90) cc_final: 0.7391 (tpt170) REVERT: D 17 LEU cc_start: 0.9015 (mt) cc_final: 0.8684 (mt) REVERT: D 140 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6485 (mt-10) REVERT: E 1 MET cc_start: 0.8578 (tpt) cc_final: 0.7532 (tpt) REVERT: F 58 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8728 (m) REVERT: F 133 MET cc_start: 0.7474 (mmt) cc_final: 0.6964 (mtt) REVERT: F 319 TYR cc_start: 0.7999 (m-80) cc_final: 0.7524 (m-80) REVERT: F 464 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7033 (tp) REVERT: F 466 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7836 (mp) REVERT: F 487 LEU cc_start: 0.6980 (mp) cc_final: 0.6532 (tt) REVERT: F 560 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.6791 (t80) REVERT: G 28 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8827 (mp) REVERT: H 8 THR cc_start: 0.8801 (t) cc_final: 0.8484 (p) REVERT: H 29 MET cc_start: 0.8001 (mtp) cc_final: 0.7675 (mtp) REVERT: H 157 ASN cc_start: 0.8541 (p0) cc_final: 0.8203 (p0) REVERT: H 292 GLU cc_start: 0.8212 (tp30) cc_final: 0.7856 (mm-30) REVERT: H 309 TYR cc_start: 0.8941 (m-80) cc_final: 0.8559 (m-10) REVERT: H 335 LYS cc_start: 0.8813 (mtmm) cc_final: 0.8426 (mtmt) REVERT: H 374 LYS cc_start: 0.7392 (mmpt) cc_final: 0.6813 (mmmt) REVERT: I 19 LYS cc_start: 0.8137 (tppt) cc_final: 0.7908 (tppt) REVERT: I 20 TYR cc_start: 0.7429 (m-80) cc_final: 0.6875 (m-80) REVERT: I 84 PHE cc_start: 0.8458 (t80) cc_final: 0.8244 (t80) REVERT: I 116 ASN cc_start: 0.8270 (m-40) cc_final: 0.8063 (m-40) REVERT: I 133 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7116 (mt-10) REVERT: J 22 GLN cc_start: 0.8323 (mp10) cc_final: 0.8065 (mp10) REVERT: J 23 ASN cc_start: 0.6621 (OUTLIER) cc_final: 0.6006 (t0) REVERT: J 168 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.5659 (p90) REVERT: K 47 MET cc_start: 0.8350 (tpt) cc_final: 0.8083 (tpp) REVERT: L 29 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.8115 (m-80) REVERT: L 59 LEU cc_start: 0.9062 (mt) cc_final: 0.8734 (mt) REVERT: N 40 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8687 (mmmt) REVERT: N 86 TYR cc_start: 0.9172 (t80) cc_final: 0.8844 (t80) REVERT: O 49 GLN cc_start: 0.8737 (tt0) cc_final: 0.8429 (tt0) REVERT: P 124 MET cc_start: 0.8569 (mtm) cc_final: 0.8187 (mtp) REVERT: P 274 MET cc_start: 0.8102 (ptp) cc_final: 0.7811 (mtm) REVERT: P 381 VAL cc_start: 0.9005 (t) cc_final: 0.8653 (p) REVERT: S 52 LYS cc_start: 0.8455 (ptmm) cc_final: 0.8243 (ptmm) REVERT: S 61 TYR cc_start: 0.8569 (t80) cc_final: 0.8157 (t80) outliers start: 158 outliers final: 132 residues processed: 854 average time/residue: 0.4543 time to fit residues: 635.3691 Evaluate side-chains 885 residues out of total 3534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 742 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 445 MET Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 560 PHE Chi-restraints excluded: chain F residue 562 ASP Chi-restraints excluded: chain F residue 587 SER Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 65 PHE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 309 THR Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain P residue 435 ASN Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 80 GLU Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 264 optimal weight: 0.0870 chunk 354 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 306 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 332 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 341 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 ASN K 80 GLN K 104 GLN K 168 ASN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.132812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.109509 restraints weight = 45769.890| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.01 r_work: 0.3003 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 34717 Z= 0.203 Angle : 0.665 15.431 47319 Z= 0.320 Chirality : 0.043 0.403 5480 Planarity : 0.005 0.109 5846 Dihedral : 9.043 118.355 5088 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.59 % Favored : 90.22 % Rotamer: Outliers : 4.45 % Allowed : 22.03 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 4234 helix: 1.05 (0.11), residues: 2380 sheet: -2.09 (0.41), residues: 161 loop : -2.76 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 454 HIS 0.004 0.001 HIS C 99 PHE 0.027 0.001 PHE H 131 TYR 0.026 0.001 TYR L 13 ARG 0.010 0.000 ARG F 578 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10947.22 seconds wall clock time: 195 minutes 9.20 seconds (11709.20 seconds total)