Starting phenix.real_space_refine on Mon Feb 19 07:24:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxh_11521/02_2024/6zxh_11521_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxh_11521/02_2024/6zxh_11521.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxh_11521/02_2024/6zxh_11521_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxh_11521/02_2024/6zxh_11521_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxh_11521/02_2024/6zxh_11521_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxh_11521/02_2024/6zxh_11521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxh_11521/02_2024/6zxh_11521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxh_11521/02_2024/6zxh_11521_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxh_11521/02_2024/6zxh_11521_updated.pdb" } resolution = 2.7 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1642 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1654 5.49 5 Mg 131 5.21 5 S 196 5.16 5 C 42056 2.51 5 N 14126 2.21 5 O 18813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 214": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 204": "OE1" <-> "OE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "G GLU 219": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 50": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "J GLU 34": "OE1" <-> "OE2" Residue "J ARG 70": "NH1" <-> "NH2" Residue "J ARG 127": "NH1" <-> "NH2" Residue "K GLU 13": "OE1" <-> "OE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "O GLU 51": "OE1" <-> "OE2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ARG 121": "NH1" <-> "NH2" Residue "O ARG 146": "NH1" <-> "NH2" Residue "O ARG 150": "NH1" <-> "NH2" Residue "P GLU 31": "OE1" <-> "OE2" Residue "P PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 118": "OE1" <-> "OE2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "R GLU 87": "OE1" <-> "OE2" Residue "Q GLU 107": "OE1" <-> "OE2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "T GLU 13": "OE1" <-> "OE2" Residue "T GLU 44": "OE1" <-> "OE2" Residue "T GLU 50": "OE1" <-> "OE2" Residue "W GLU 49": "OE1" <-> "OE2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 139": "OE1" <-> "OE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y GLU 42": "OE1" <-> "OE2" Residue "U GLU 107": "OE1" <-> "OE2" Residue "U GLU 113": "OE1" <-> "OE2" Residue "Z GLU 90": "OE1" <-> "OE2" Residue "b GLU 75": "OE1" <-> "OE2" Residue "c GLU 62": "OE1" <-> "OE2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "d ARG 12": "NH1" <-> "NH2" Residue "g GLU 49": "OE1" <-> "OE2" Residue "g GLU 145": "OE1" <-> "OE2" Residue "g GLU 149": "OE1" <-> "OE2" Residue "g GLU 262": "OE1" <-> "OE2" Residue "j GLU 17": "OE1" <-> "OE2" Residue "j GLU 99": "OE1" <-> "OE2" Residue "z GLU 137": "OE1" <-> "OE2" Residue "z GLU 227": "OE1" <-> "OE2" Residue "z ARG 231": "NH1" <-> "NH2" Residue "z ARG 240": "NH1" <-> "NH2" Residue "z GLU 327": "OE1" <-> "OE2" Residue "z ARG 358": "NH1" <-> "NH2" Residue "z GLU 383": "OE1" <-> "OE2" Residue "z GLU 404": "OE1" <-> "OE2" Residue "z GLU 422": "OE1" <-> "OE2" Residue "z ARG 546": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 76979 Number of models: 1 Model: "" Number of chains: 44 Chain: "2" Number of atoms: 35310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1651, 35310 Classifications: {'RNA': 1651} Modifications used: {'rna2p': 4, 'rna2p_pur': 140, 'rna2p_pyr': 110, 'rna3p': 58, 'rna3p_pur': 715, 'rna3p_pyr': 612} Link IDs: {'rna2p': 253, 'rna3p': 1397} Chain breaks: 13 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 41 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "B" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1715 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "C" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1674 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "h" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 792 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "E" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2031 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 14, 'TRANS': 240} Chain: "D" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1745 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "G" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1802 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 10, 'TRANS': 212} Chain: "H" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1446 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 3 Chain: "I" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1638 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 1 Chain: "J" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1465 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Chain: "F" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1461 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 1 Chain: "L" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1127 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 Chain: "K" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 799 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 947 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 2 Chain: "P" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1077 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1116 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "S" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1162 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 137} 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: "T" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1094 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "V" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1080 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "Y" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 987 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "U" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} 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: "Z" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 638 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 79} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "b" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 611 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Chain: "c" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "d" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 450 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "e" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 398 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 1 Chain: "f" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 465 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain breaks: 1 Chain: "g" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2306 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 10, 'TRANS': 284} Chain breaks: 3 Chain: "j" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 934 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "z" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2803 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 11, 'TRANS': 337} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "2" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 132 Unusual residues: {' MG': 124} Classifications: {'peptide': 1, 'undetermined': 124} Link IDs: {None: 124} Chain: "h" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 40582 SG CYS h 23 91.506 169.485 100.603 1.00 5.81 S ATOM 40603 SG CYS h 26 91.087 168.383 96.507 1.00 6.82 S ATOM 40986 SG CYS h 74 93.192 166.262 99.272 1.00 5.81 S ATOM 41005 SG CYS h 77 94.574 169.440 98.151 1.00 6.42 S ATOM 69616 SG CYS d 21 162.907 154.585 70.466 1.00 5.81 S ATOM 69640 SG CYS d 24 160.007 152.027 69.281 1.00 5.81 S ATOM 69761 SG CYS d 39 159.016 155.599 71.103 1.00 5.81 S ATOM 69787 SG CYS d 42 160.550 152.500 73.215 1.00 5.81 S ATOM 70551 SG CYS f 121 189.537 142.819 29.455 1.00 21.86 S ATOM 70587 SG CYS f 126 187.911 141.459 33.416 1.00 26.76 S ATOM 70705 SG CYS f 141 186.096 141.385 30.113 1.00 21.97 S ATOM 70724 SG CYS f 144 186.824 144.663 31.767 1.00 24.77 S Time building chain proxies: 31.51, per 1000 atoms: 0.41 Number of scatterers: 76979 At special positions: 0 Unit cell: (219.213, 247.806, 193.797, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 196 16.00 P 1654 15.00 Mg 131 11.99 O 18813 8.00 N 14126 7.00 C 42056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 249 " distance=2.04 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=0, symmetry=0 Time building additional restraints: 30.20 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d 101 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 42 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 21 " pdb=" ZN f 500 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 144 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 121 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 126 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 141 " pdb=" ZN h 201 " pdb="ZN ZN h 201 " - pdb=" SG CYS h 26 " pdb="ZN ZN h 201 " - pdb=" SG CYS h 74 " pdb="ZN ZN h 201 " - pdb=" SG CYS h 77 " pdb="ZN ZN h 201 " - pdb=" SG CYS h 23 " Number of angles added : 18 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9674 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 174 helices and 58 sheets defined 31.1% alpha, 17.0% beta 461 base pairs and 881 stacking pairs defined. Time for finding SS restraints: 31.49 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 81 through 94 removed outlier: 5.575A pdb=" N ARG A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 87 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 168 through 186 Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'B' and resid 24 through 26 No H-bonds generated for 'chain 'B' and resid 24 through 26' Processing helix chain 'B' and resid 71 through 74 No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 158 through 177 Processing helix chain 'B' and resid 181 through 189 removed outlier: 3.514A pdb=" N ASN B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 200 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 147 through 160 Processing helix chain 'C' and resid 208 through 216 Processing helix chain 'C' and resid 233 through 248 removed outlier: 3.994A pdb=" N THR C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TYR C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 265 through 268 No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'h' and resid 50 through 56 removed outlier: 3.617A pdb=" N GLU h 55 " --> pdb=" O ARG h 51 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA h 56 " --> pdb=" O ASP h 52 " (cutoff:3.500A) Processing helix chain 'h' and resid 75 through 80 Processing helix chain 'h' and resid 91 through 93 No H-bonds generated for 'chain 'h' and resid 91 through 93' Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 58 through 67 removed outlier: 3.834A pdb=" N GLN E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 248 through 255 Processing helix chain 'D' and resid 7 through 32 removed outlier: 3.585A pdb=" N VAL D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLU D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.801A pdb=" N LEU D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 55 through 59' Processing helix chain 'D' and resid 64 through 76 Processing helix chain 'D' and resid 98 through 109 Processing helix chain 'D' and resid 115 through 129 Processing helix chain 'D' and resid 162 through 167 removed outlier: 4.096A pdb=" N TYR D 167 " --> pdb=" O VAL D 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 145 Processing helix chain 'G' and resid 182 through 222 Processing helix chain 'H' and resid 18 through 30 removed outlier: 3.827A pdb=" N LEU H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 73 removed outlier: 5.356A pdb=" N LYS H 70 " --> pdb=" O PRO H 67 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN H 73 " --> pdb=" O LYS H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 118 through 120 No H-bonds generated for 'chain 'H' and resid 118 through 120' Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 160 through 166 removed outlier: 6.305A pdb=" N ASN H 164 " --> pdb=" O ALA H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 180 Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 107 through 116 Processing helix chain 'I' and resid 132 through 137 Processing helix chain 'I' and resid 143 through 155 removed outlier: 4.743A pdb=" N ASN I 155 " --> pdb=" O GLU I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 168 removed outlier: 3.723A pdb=" N GLN I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 182 No H-bonds generated for 'chain 'I' and resid 179 through 182' Processing helix chain 'I' and resid 192 through 205 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 40 through 60 Processing helix chain 'J' and resid 68 through 84 Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 95 through 99 removed outlier: 3.515A pdb=" N GLY J 99 " --> pdb=" O TYR J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 106 Processing helix chain 'J' and resid 110 through 116 Processing helix chain 'J' and resid 123 through 132 removed outlier: 3.718A pdb=" N GLN J 132 " --> pdb=" O VAL J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 153 No H-bonds generated for 'chain 'J' and resid 151 through 153' Processing helix chain 'J' and resid 172 through 177 Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 86 through 104 removed outlier: 3.562A pdb=" N ARG F 91 " --> pdb=" O LEU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 119 Processing helix chain 'F' and resid 143 through 158 removed outlier: 4.770A pdb=" N GLY F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 169 through 181 Processing helix chain 'F' and resid 189 through 202 removed outlier: 3.837A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 51 No H-bonds generated for 'chain 'L' and resid 48 through 51' Processing helix chain 'K' and resid 5 through 18 removed outlier: 3.593A pdb=" N GLU K 18 " --> pdb=" O LEU K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 54 Processing helix chain 'K' and resid 73 through 83 removed outlier: 3.591A pdb=" N GLN K 77 " --> pdb=" O ASN K 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 47 through 57 Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 71 through 78 Processing helix chain 'N' and resid 86 through 104 Processing helix chain 'N' and resid 109 through 131 Processing helix chain 'N' and resid 143 through 149 removed outlier: 4.470A pdb=" N SER N 147 " --> pdb=" O SER N 143 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ALA N 148 " --> pdb=" O SER N 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 67 No H-bonds generated for 'chain 'O' and resid 65 through 67' Processing helix chain 'O' and resid 71 through 88 removed outlier: 3.516A pdb=" N LEU O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 121 Processing helix chain 'M' and resid 19 through 27 Processing helix chain 'M' and resid 35 through 43 Processing helix chain 'M' and resid 61 through 71 removed outlier: 4.200A pdb=" N VAL M 65 " --> pdb=" O TYR M 61 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU M 66 " --> pdb=" O VAL M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 89 Processing helix chain 'M' and resid 120 through 128 removed outlier: 4.281A pdb=" N PHE M 128 " --> pdb=" O ILE M 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 26 Processing helix chain 'P' and resid 30 through 36 removed outlier: 4.278A pdb=" N GLN P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU P 36 " --> pdb=" O GLN P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 47 Processing helix chain 'P' and resid 51 through 65 Processing helix chain 'P' and resid 87 through 89 No H-bonds generated for 'chain 'P' and resid 87 through 89' Processing helix chain 'P' and resid 109 through 111 No H-bonds generated for 'chain 'P' and resid 109 through 111' Processing helix chain 'P' and resid 116 through 118 No H-bonds generated for 'chain 'P' and resid 116 through 118' Processing helix chain 'P' and resid 139 through 141 No H-bonds generated for 'chain 'P' and resid 139 through 141' Processing helix chain 'R' and resid 7 through 17 Processing helix chain 'R' and resid 21 through 23 No H-bonds generated for 'chain 'R' and resid 21 through 23' Processing helix chain 'R' and resid 28 through 38 removed outlier: 3.634A pdb=" N ARG R 33 " --> pdb=" O HIS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 63 removed outlier: 4.036A pdb=" N ARG R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 81 removed outlier: 3.625A pdb=" N ARG R 81 " --> pdb=" O GLU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 108 Processing helix chain 'Q' and resid 39 through 41 No H-bonds generated for 'chain 'Q' and resid 39 through 41' Processing helix chain 'Q' and resid 45 through 52 removed outlier: 4.728A pdb=" N TYR Q 49 " --> pdb=" O THR Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 58 No H-bonds generated for 'chain 'Q' and resid 55 through 58' Processing helix chain 'Q' and resid 60 through 63 No H-bonds generated for 'chain 'Q' and resid 60 through 63' Processing helix chain 'Q' and resid 77 through 98 Processing helix chain 'Q' and resid 105 through 115 Processing helix chain 'Q' and resid 117 through 119 No H-bonds generated for 'chain 'Q' and resid 117 through 119' Processing helix chain 'S' and resid 26 through 32 removed outlier: 4.377A pdb=" N THR S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA S 32 " --> pdb=" O PHE S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 47 removed outlier: 3.597A pdb=" N VAL S 43 " --> pdb=" O ARG S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 58 No H-bonds generated for 'chain 'S' and resid 56 through 58' Processing helix chain 'S' and resid 61 through 72 Processing helix chain 'S' and resid 75 through 77 No H-bonds generated for 'chain 'S' and resid 75 through 77' Processing helix chain 'S' and resid 103 through 116 Processing helix chain 'S' and resid 120 through 126 Processing helix chain 'T' and resid 6 through 8 No H-bonds generated for 'chain 'T' and resid 6 through 8' Processing helix chain 'T' and resid 11 through 25 Processing helix chain 'T' and resid 52 through 66 Processing helix chain 'T' and resid 72 through 78 removed outlier: 3.546A pdb=" N LYS T 77 " --> pdb=" O GLY T 73 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 109 Processing helix chain 'T' and resid 125 through 140 removed outlier: 3.607A pdb=" N ILE T 134 " --> pdb=" O ASP T 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 61 Processing helix chain 'V' and resid 65 through 75 Processing helix chain 'W' and resid 6 through 20 Processing helix chain 'W' and resid 32 through 43 Processing helix chain 'W' and resid 83 through 93 removed outlier: 3.789A pdb=" N LEU W 86 " --> pdb=" O LEU W 83 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU W 87 " --> pdb=" O LYS W 84 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS W 88 " --> pdb=" O ASP W 85 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN W 91 " --> pdb=" O LYS W 88 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU W 93 " --> pdb=" O GLN W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 118 Processing helix chain 'X' and resid 10 through 23 removed outlier: 4.519A pdb=" N TRP X 22 " --> pdb=" O ARG X 18 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N HIS X 23 " --> pdb=" O ASP X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 31 Processing helix chain 'X' and resid 34 through 38 Processing helix chain 'X' and resid 90 through 93 Processing helix chain 'X' and resid 130 through 134 Processing helix chain 'Y' and resid 37 through 48 Processing helix chain 'Y' and resid 79 through 85 Processing helix chain 'Y' and resid 88 through 92 Processing helix chain 'Y' and resid 104 through 116 removed outlier: 4.135A pdb=" N LYS Y 116 " --> pdb=" O ASN Y 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 119 through 124 Processing helix chain 'U' and resid 29 through 44 Processing helix chain 'U' and resid 95 through 103 removed outlier: 3.752A pdb=" N SER U 103 " --> pdb=" O LYS U 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 60 removed outlier: 3.703A pdb=" N ASP Z 56 " --> pdb=" O LYS Z 52 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS Z 57 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 64 No H-bonds generated for 'chain 'Z' and resid 62 through 64' Processing helix chain 'Z' and resid 70 through 77 Processing helix chain 'Z' and resid 81 through 93 removed outlier: 3.528A pdb=" N SER Z 93 " --> pdb=" O GLN Z 89 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 17 Processing helix chain 'd' and resid 33 through 35 No H-bonds generated for 'chain 'd' and resid 33 through 35' Processing helix chain 'd' and resid 40 through 50 removed outlier: 5.577A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 15 Processing helix chain 'e' and resid 31 through 42 Processing helix chain 'j' and resid 3 through 14 removed outlier: 3.999A pdb=" N ARG j 7 " --> pdb=" O GLN j 3 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS j 8 " --> pdb=" O ALA j 4 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) Processing helix chain 'j' and resid 92 through 99 Processing helix chain 'z' and resid 131 through 146 removed outlier: 3.791A pdb=" N MET z 146 " --> pdb=" O LYS z 142 " (cutoff:3.500A) Processing helix chain 'z' and resid 152 through 155 Processing helix chain 'z' and resid 164 through 176 removed outlier: 3.616A pdb=" N ARG z 176 " --> pdb=" O LYS z 172 " (cutoff:3.500A) Processing helix chain 'z' and resid 228 through 230 No H-bonds generated for 'chain 'z' and resid 228 through 230' Processing helix chain 'z' and resid 239 through 259 Processing helix chain 'z' and resid 290 through 292 No H-bonds generated for 'chain 'z' and resid 290 through 292' Processing helix chain 'z' and resid 297 through 316 Processing helix chain 'z' and resid 353 through 369 removed outlier: 3.558A pdb=" N PHE z 367 " --> pdb=" O ASN z 363 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE z 368 " --> pdb=" O VAL z 364 " (cutoff:3.500A) Processing helix chain 'z' and resid 378 through 386 Processing helix chain 'z' and resid 395 through 407 Processing helix chain 'z' and resid 411 through 426 removed outlier: 3.737A pdb=" N SER z 415 " --> pdb=" O LYS z 411 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU z 423 " --> pdb=" O HIS z 419 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL z 424 " --> pdb=" O VAL z 420 " (cutoff:3.500A) Processing helix chain 'z' and resid 439 through 451 Processing helix chain 'z' and resid 533 through 548 removed outlier: 4.129A pdb=" N ASN z 548 " --> pdb=" O GLU z 544 " (cutoff:3.500A) Processing helix chain 'z' and resid 552 through 558 Processing sheet with id= A, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.386A pdb=" N LEU A 121 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE A 77 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 123 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL A 124 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 145 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A 159 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS A 148 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE A 161 " --> pdb=" O CYS A 148 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.910A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.502A pdb=" N ASP B 90 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 66 through 70 removed outlier: 5.363A pdb=" N ILE B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE B 100 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 13.371A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 12.640A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 137 through 144 removed outlier: 3.598A pdb=" N LYS C 108 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 184 through 188 Processing sheet with id= G, first strand: chain 'h' and resid 20 through 22 Processing sheet with id= H, first strand: chain 'h' and resid 36 through 43 Processing sheet with id= I, first strand: chain 'E' and resid 70 through 72 Processing sheet with id= J, first strand: chain 'E' and resid 121 through 125 removed outlier: 6.683A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 Processing sheet with id= L, first strand: chain 'E' and resid 225 through 227 removed outlier: 6.762A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 84 through 90 removed outlier: 7.093A pdb=" N THR D 46 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N TYR D 87 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE D 48 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLU D 89 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE D 50 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 148 through 155 removed outlier: 3.767A pdb=" N GLY D 133 " --> pdb=" O MET D 189 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.758A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 72 through 77 Processing sheet with id= Q, first strand: chain 'G' and resid 159 through 162 removed outlier: 3.870A pdb=" N ARG G 170 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 54 through 57 removed outlier: 3.887A pdb=" N GLY G 54 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL G 108 " --> pdb=" O ASN G 56 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 91 through 96 removed outlier: 3.872A pdb=" N HIS H 91 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 185 through 188 removed outlier: 8.177A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 62 through 67 Processing sheet with id= V, first strand: chain 'I' and resid 187 through 189 removed outlier: 6.703A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 42 through 48 removed outlier: 6.616A pdb=" N HIS I 44 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ALA I 57 " --> pdb=" O HIS I 44 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL I 46 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR I 55 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL I 48 " --> pdb=" O LYS I 53 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LYS I 53 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 135 through 137 Processing sheet with id= Y, first strand: chain 'F' and resid 123 through 127 Processing sheet with id= Z, first strand: chain 'L' and resid 101 through 112 removed outlier: 6.224A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 15.604A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 16.693A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 20 through 23 Processing sheet with id= AB, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.835A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA O 92 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS O 31 " --> pdb=" O ALA O 92 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS O 94 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE O 33 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS O 96 " --> pdb=" O ILE O 33 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ALA O 35 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG O 98 " --> pdb=" O ALA O 35 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'M' and resid 31 through 33 removed outlier: 3.670A pdb=" N VAL M 110 " --> pdb=" O ALA M 32 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'P' and resid 76 through 78 Processing sheet with id= AE, first strand: chain 'R' and resid 96 through 98 Processing sheet with id= AF, first strand: chain 'Q' and resid 9 through 15 Processing sheet with id= AG, first strand: chain 'S' and resid 12 through 15 Processing sheet with id= AH, first strand: chain 'T' and resid 81 through 83 Processing sheet with id= AI, first strand: chain 'T' and resid 113 through 115 Processing sheet with id= AJ, first strand: chain 'V' and resid 32 through 37 Processing sheet with id= AK, first strand: chain 'W' and resid 24 through 27 Processing sheet with id= AL, first strand: chain 'W' and resid 72 through 74 removed outlier: 6.833A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE W 128 " --> pdb=" O PHE W 101 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 80 through 84 removed outlier: 3.662A pdb=" N GLU X 53 " --> pdb=" O ARG X 71 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ALA X 103 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL X 122 " --> pdb=" O ALA X 103 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'Y' and resid 6 through 10 Processing sheet with id= AO, first strand: chain 'Y' and resid 13 through 15 Processing sheet with id= AP, first strand: chain 'U' and resid 111 through 115 removed outlier: 4.138A pdb=" N LYS U 49 " --> pdb=" O HIS U 92 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'U' and resid 59 through 66 Processing sheet with id= AR, first strand: chain 'Z' and resid 97 through 101 removed outlier: 6.800A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'b' and resid 43 through 47 Processing sheet with id= AT, first strand: chain 'c' and resid 55 through 58 removed outlier: 6.590A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL c 17 " --> pdb=" O GLN c 29 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLN c 29 " --> pdb=" O VAL c 17 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'c' and resid 19 through 21 Processing sheet with id= AV, first strand: chain 'f' and resid 132 through 135 removed outlier: 3.531A pdb=" N LEU f 146 " --> pdb=" O CYS f 141 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'g' and resid 18 through 23 removed outlier: 6.744A pdb=" N ALA g 34 " --> pdb=" O THR g 19 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE g 21 " --> pdb=" O LEU g 32 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU g 32 " --> pdb=" O ILE g 21 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR g 23 " --> pdb=" O MET g 30 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N MET g 30 " --> pdb=" O THR g 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER g 35 " --> pdb=" O THR g 39 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR g 39 " --> pdb=" O SER g 35 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG g 57 " --> pdb=" O MET g 42 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'g' and resid 66 through 71 removed outlier: 6.688A pdb=" N GLY g 81 " --> pdb=" O SER g 67 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL g 69 " --> pdb=" O LEU g 79 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU g 79 " --> pdb=" O VAL g 69 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE g 71 " --> pdb=" O PHE g 77 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE g 77 " --> pdb=" O ILE g 71 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP g 91 " --> pdb=" O THR g 97 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N THR g 97 " --> pdb=" O ASP g 91 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'g' and resid 108 through 113 removed outlier: 7.058A pdb=" N GLY g 123 " --> pdb=" O LEU g 109 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N VAL g 111 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL g 121 " --> pdb=" O VAL g 111 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER g 124 " --> pdb=" O THR g 128 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'g' and resid 151 through 156 removed outlier: 6.831A pdb=" N CYS g 168 " --> pdb=" O SER g 152 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL g 154 " --> pdb=" O VAL g 166 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL g 166 " --> pdb=" O VAL g 154 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE g 156 " --> pdb=" O ILE g 164 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE g 164 " --> pdb=" O PHE g 156 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'g' and resid 195 through 200 removed outlier: 7.126A pdb=" N GLY g 210 " --> pdb=" O ASN g 196 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL g 198 " --> pdb=" O ALA g 208 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA g 208 " --> pdb=" O VAL g 198 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL g 200 " --> pdb=" O LEU g 206 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU g 206 " --> pdb=" O VAL g 200 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP g 220 " --> pdb=" O HIS g 226 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N HIS g 226 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'g' and resid 238 through 241 removed outlier: 3.790A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP g 268 " --> pdb=" O ILE g 258 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASP g 260 " --> pdb=" O ILE g 266 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE g 266 " --> pdb=" O ASP g 260 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'g' and resid 6 through 11 removed outlier: 6.884A pdb=" N VAL g 309 " --> pdb=" O ARG g 8 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR g 10 " --> pdb=" O VAL g 307 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL g 307 " --> pdb=" O THR g 10 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'j' and resid 68 through 71 removed outlier: 6.737A pdb=" N GLU j 40 " --> pdb=" O LEU j 31 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N SER j 52 " --> pdb=" O LYS j 81 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU j 83 " --> pdb=" O SER j 52 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE j 70 " --> pdb=" O SER j 85 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL j 87 " --> pdb=" O PHE j 68 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N PHE j 68 " --> pdb=" O VAL j 87 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'z' and resid 267 through 271 removed outlier: 6.731A pdb=" N VAL z 276 " --> pdb=" O ILE z 268 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU z 270 " --> pdb=" O VAL z 274 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL z 274 " --> pdb=" O LEU z 270 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER z 187 " --> pdb=" O VAL z 194 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N HIS z 196 " --> pdb=" O CYS z 185 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N CYS z 185 " --> pdb=" O HIS z 196 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'z' and resid 330 through 333 1399 hydrogen bonds defined for protein. 3966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1160 hydrogen bonds 1834 hydrogen bond angles 0 basepair planarities 461 basepair parallelities 881 stacking parallelities Total time for adding SS restraints: 60.18 Time building geometry restraints manager: 32.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 8211 1.27 - 1.40: 23812 1.40 - 1.54: 45898 1.54 - 1.68: 3493 1.68 - 1.82: 304 Bond restraints: 81718 Sorted by residual: bond pdb=" C4' A2M 2 668 " pdb=" O4' A2M 2 668 " ideal model delta sigma weight residual 1.558 1.278 0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C4' A2M 2 484 " pdb=" O4' A2M 2 484 " ideal model delta sigma weight residual 1.558 1.292 0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" C4' A2M 2 159 " pdb=" C3' A2M 2 159 " ideal model delta sigma weight residual 1.276 1.539 -0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C4' A2M 21678 " pdb=" O4' A2M 21678 " ideal model delta sigma weight residual 1.558 1.296 0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C4' A2M 21383 " pdb=" C3' A2M 21383 " ideal model delta sigma weight residual 1.276 1.536 -0.260 2.00e-02 2.50e+03 1.69e+02 ... (remaining 81713 not shown) Histogram of bond angle deviations from ideal: 41.68 - 65.53: 9 65.53 - 89.37: 27 89.37 - 113.21: 56239 113.21 - 137.05: 61831 137.05 - 160.89: 30 Bond angle restraints: 118136 Sorted by residual: angle pdb=" C3' A2M 2 668 " pdb=" O3' A2M 2 668 " pdb=" P A 2 669 " ideal model delta sigma weight residual 120.20 159.31 -39.11 1.50e+00 4.44e-01 6.80e+02 angle pdb=" O3' A2M 21678 " pdb=" P A 21679 " pdb=" O5' A 21679 " ideal model delta sigma weight residual 104.00 141.84 -37.84 1.50e+00 4.44e-01 6.36e+02 angle pdb=" O3' A 21030 " pdb=" P A2M 21031 " pdb=" O5' A2M 21031 " ideal model delta sigma weight residual 104.00 68.68 35.32 1.50e+00 4.44e-01 5.54e+02 angle pdb=" C3' A2M 2 166 " pdb=" O3' A2M 2 166 " pdb=" P G 2 167 " ideal model delta sigma weight residual 120.20 153.67 -33.47 1.50e+00 4.44e-01 4.98e+02 angle pdb=" O3' A 2 435 " pdb=" P OMG 2 436 " pdb=" OP1 OMG 2 436 " ideal model delta sigma weight residual 108.00 41.68 66.32 3.00e+00 1.11e-01 4.89e+02 ... (remaining 118131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 47084 35.96 - 71.92: 4174 71.92 - 107.88: 572 107.88 - 143.84: 18 143.84 - 179.80: 40 Dihedral angle restraints: 51888 sinusoidal: 36927 harmonic: 14961 Sorted by residual: dihedral pdb=" CA SER O 137 " pdb=" C SER O 137 " pdb=" N ASP O 138 " pdb=" CA ASP O 138 " ideal model delta harmonic sigma weight residual 180.00 130.09 49.91 0 5.00e+00 4.00e-02 9.96e+01 dihedral pdb=" C5' G 21814 " pdb=" C4' G 21814 " pdb=" C3' G 21814 " pdb=" O3' G 21814 " ideal model delta sinusoidal sigma weight residual 147.00 80.09 66.91 1 8.00e+00 1.56e-02 9.12e+01 dihedral pdb=" C4' G 21814 " pdb=" C3' G 21814 " pdb=" C2' G 21814 " pdb=" C1' G 21814 " ideal model delta sinusoidal sigma weight residual -35.00 31.38 -66.38 1 8.00e+00 1.56e-02 8.99e+01 ... (remaining 51885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 13153 0.097 - 0.194: 1065 0.194 - 0.291: 60 0.291 - 0.387: 15 0.387 - 0.484: 4 Chirality restraints: 14297 Sorted by residual: chirality pdb=" CB VAL h 84 " pdb=" CA VAL h 84 " pdb=" CG1 VAL h 84 " pdb=" CG2 VAL h 84 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" CG LEU Y 18 " pdb=" CB LEU Y 18 " pdb=" CD1 LEU Y 18 " pdb=" CD2 LEU Y 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" C3' G 21065 " pdb=" C4' G 21065 " pdb=" O3' G 21065 " pdb=" C2' G 21065 " both_signs ideal model delta sigma weight residual False -2.48 -2.08 -0.40 2.00e-01 2.50e+01 3.95e+00 ... (remaining 14294 not shown) Planarity restraints: 8884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 683 " 0.138 2.00e-02 2.50e+03 6.98e-01 1.10e+04 pdb=" C4' OMG 2 683 " 0.520 2.00e-02 2.50e+03 pdb=" O4' OMG 2 683 " 0.715 2.00e-02 2.50e+03 pdb=" C3' OMG 2 683 " -0.509 2.00e-02 2.50e+03 pdb=" O3' OMG 2 683 " -0.800 2.00e-02 2.50e+03 pdb=" C2' OMG 2 683 " -0.111 2.00e-02 2.50e+03 pdb=" O2' OMG 2 683 " 1.113 2.00e-02 2.50e+03 pdb=" C1' OMG 2 683 " 0.124 2.00e-02 2.50e+03 pdb=" N9 OMG 2 683 " -1.189 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' A2M 21383 " -0.010 2.00e-02 2.50e+03 6.68e-01 1.00e+04 pdb=" C4' A2M 21383 " -0.492 2.00e-02 2.50e+03 pdb=" O4' A2M 21383 " -0.715 2.00e-02 2.50e+03 pdb=" C3' A2M 21383 " 0.629 2.00e-02 2.50e+03 pdb=" O3' A2M 21383 " 0.767 2.00e-02 2.50e+03 pdb=" C2' A2M 21383 " 0.124 2.00e-02 2.50e+03 pdb=" O2' A2M 21383 " -1.113 2.00e-02 2.50e+03 pdb=" C1' A2M 21383 " -0.186 2.00e-02 2.50e+03 pdb=" N9 A2M 21383 " 0.995 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' A2M 2 166 " -0.025 2.00e-02 2.50e+03 6.42e-01 9.28e+03 pdb=" C4' A2M 2 166 " -0.465 2.00e-02 2.50e+03 pdb=" O4' A2M 2 166 " -0.623 2.00e-02 2.50e+03 pdb=" C3' A2M 2 166 " 0.641 2.00e-02 2.50e+03 pdb=" O3' A2M 2 166 " 0.742 2.00e-02 2.50e+03 pdb=" C2' A2M 2 166 " 0.124 2.00e-02 2.50e+03 pdb=" O2' A2M 2 166 " -1.109 2.00e-02 2.50e+03 pdb=" C1' A2M 2 166 " -0.209 2.00e-02 2.50e+03 pdb=" N9 A2M 2 166 " 0.925 2.00e-02 2.50e+03 ... (remaining 8881 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 434 2.52 - 3.12: 50096 3.12 - 3.71: 135672 3.71 - 4.31: 207623 4.31 - 4.90: 290654 Nonbonded interactions: 684479 Sorted by model distance: nonbonded pdb=" OP2 A2M 2 668 " pdb="MG MG 21955 " model vdw 1.930 2.170 nonbonded pdb=" OP2 G 21603 " pdb="MG MG 21912 " model vdw 1.975 2.170 nonbonded pdb=" O6 G 21517 " pdb="MG MG 21992 " model vdw 1.981 2.170 nonbonded pdb=" OP1 A2M 2 27 " pdb="MG MG 21927 " model vdw 2.003 2.170 nonbonded pdb=" OP2 U 2 100 " pdb="MG MG 21929 " model vdw 2.005 2.170 ... (remaining 684474 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.350 Construct map_model_manager: 0.060 Extract box with map and model: 12.300 Check model and map are aligned: 0.880 Set scattering table: 0.550 Process input model: 225.630 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 259.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.012 0.280 81718 Z= 0.730 Angle : 1.450 66.315 118136 Z= 0.650 Chirality : 0.055 0.484 14297 Planarity : 0.040 0.698 8884 Dihedral : 22.643 179.797 42211 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 0.45 % Allowed : 5.57 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.39 (0.10), residues: 5088 helix: -1.91 (0.10), residues: 1690 sheet: -0.78 (0.16), residues: 901 loop : -1.58 (0.11), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP g 291 HIS 0.027 0.002 HIS S 135 PHE 0.062 0.004 PHE C 236 TYR 0.025 0.003 TYR f 105 ARG 0.014 0.001 ARG O 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 976 time to evaluate : 4.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 188 ASN cc_start: 0.8524 (m-40) cc_final: 0.8281 (m-40) REVERT: G 1 MET cc_start: 0.7589 (ttm) cc_final: 0.7319 (ttp) REVERT: H 32 MET cc_start: 0.4052 (mpp) cc_final: 0.3780 (mtm) REVERT: J 72 PHE cc_start: 0.7840 (t80) cc_final: 0.7629 (t80) REVERT: F 188 TYR cc_start: 0.8068 (t80) cc_final: 0.7775 (t80) REVERT: L 80 MET cc_start: 0.7973 (mtm) cc_final: 0.7740 (mtm) REVERT: P 93 MET cc_start: 0.8002 (mmm) cc_final: 0.7737 (mmm) REVERT: R 118 GLN cc_start: 0.7805 (tt0) cc_final: 0.7591 (pt0) REVERT: Q 41 MET cc_start: 0.8674 (mmt) cc_final: 0.8289 (mmt) REVERT: Y 72 PHE cc_start: 0.8253 (m-80) cc_final: 0.7906 (t80) REVERT: U 81 GLN cc_start: 0.8701 (pt0) cc_final: 0.8455 (pt0) REVERT: j 60 ASN cc_start: 0.8020 (m-40) cc_final: 0.7737 (m110) REVERT: j 64 LYS cc_start: 0.8020 (pttm) cc_final: 0.7802 (ptmm) REVERT: z 251 MET cc_start: 0.8228 (tpt) cc_final: 0.7946 (tpt) REVERT: z 277 MET cc_start: 0.8600 (ptt) cc_final: 0.8305 (ptt) outliers start: 20 outliers final: 9 residues processed: 987 average time/residue: 1.8992 time to fit residues: 2376.0781 Evaluate side-chains 773 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 764 time to evaluate : 4.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain c residue 46 VAL Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 424 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 563 optimal weight: 6.9990 chunk 505 optimal weight: 0.7980 chunk 280 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 341 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 chunk 522 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 317 optimal weight: 0.9980 chunk 389 optimal weight: 3.9990 chunk 605 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 132 GLN C 113 GLN h 80 HIS E 8 HIS E 50 ASN E 161 GLN E 216 ASN D 101 GLN D 207 HIS G 56 ASN G 59 GLN G 110 ASN G 155 GLN H 73 GLN H 91 HIS H 193 GLN I 116 HIS I 165 GLN J 113 GLN J 132 GLN F 29 GLN F 79 HIS F 83 ASN F 107 ASN L 108 ASN ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 GLN N 105 ASN O 38 ASN M 15 ASN M 46 GLN P 41 GLN P 79 HIS R 31 ASN R 74 GLN R 93 GLN Q 11 GLN Q 35 ASN Q 80 GLN S 101 ASN S 120 HIS T 12 GLN T 91 HIS V 29 HIS V 35 ASN W 16 ASN W 113 HIS X 73 GLN X 97 ASN Y 22 GLN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 HIS b 26 GLN d 45 GLN e 56 ASN f 135 HIS f 139 HIS g 51 ASN g 64 HIS g 117 ASN g 178 ASN g 222 ASN g 237 ASN j 25 GLN ** z 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 306 GLN z 316 GLN z 322 HIS z 363 ASN z 365 ASN ** z 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 81718 Z= 0.200 Angle : 0.960 34.138 118136 Z= 0.488 Chirality : 0.040 0.338 14297 Planarity : 0.009 0.136 8884 Dihedral : 23.836 179.570 31525 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.41 % Allowed : 13.79 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.14 (0.11), residues: 5088 helix: -0.36 (0.12), residues: 1680 sheet: -0.39 (0.16), residues: 884 loop : -1.10 (0.11), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP g 132 HIS 0.009 0.001 HIS S 135 PHE 0.029 0.001 PHE C 236 TYR 0.017 0.001 TYR T 65 ARG 0.008 0.000 ARG H 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 813 time to evaluate : 4.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.7671 (mtpp) cc_final: 0.7444 (tttm) REVERT: D 143 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6331 (tmt90) REVERT: G 1 MET cc_start: 0.7571 (ttm) cc_final: 0.7337 (ttp) REVERT: F 188 TYR cc_start: 0.7949 (t80) cc_final: 0.7722 (t80) REVERT: L 8 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7402 (mtm180) REVERT: K 60 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7384 (tt0) REVERT: O 124 MET cc_start: 0.8308 (mmm) cc_final: 0.8085 (mmm) REVERT: P 83 MET cc_start: 0.8271 (tpt) cc_final: 0.7857 (tpt) REVERT: Q 41 MET cc_start: 0.8572 (mmt) cc_final: 0.8175 (mmt) REVERT: Q 129 SER cc_start: 0.8421 (m) cc_final: 0.8103 (p) REVERT: S 106 LYS cc_start: 0.8705 (mmtp) cc_final: 0.8431 (mmpt) REVERT: V 51 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.7988 (mmmt) REVERT: Y 72 PHE cc_start: 0.8169 (m-80) cc_final: 0.7919 (t80) REVERT: U 81 GLN cc_start: 0.8623 (pt0) cc_final: 0.8396 (pt0) REVERT: j 32 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7548 (ttm-80) REVERT: j 64 LYS cc_start: 0.7976 (pttm) cc_final: 0.7753 (pttp) REVERT: j 78 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7075 (tt0) REVERT: z 251 MET cc_start: 0.8141 (tpt) cc_final: 0.7931 (tpt) REVERT: z 277 MET cc_start: 0.8517 (ptt) cc_final: 0.8260 (ptt) REVERT: z 376 MET cc_start: 0.7847 (mtp) cc_final: 0.7559 (mtm) outliers start: 108 outliers final: 39 residues processed: 867 average time/residue: 1.8141 time to fit residues: 2016.4565 Evaluate side-chains 787 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 743 time to evaluate : 4.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 193 LYS Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain M residue 48 HIS Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain V residue 51 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain j residue 32 ARG Chi-restraints excluded: chain j residue 78 GLU Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 215 LEU Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 424 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 336 optimal weight: 0.4980 chunk 187 optimal weight: 0.0970 chunk 504 optimal weight: 8.9990 chunk 412 optimal weight: 0.0970 chunk 167 optimal weight: 8.9990 chunk 606 optimal weight: 10.0000 chunk 655 optimal weight: 6.9990 chunk 540 optimal weight: 9.9990 chunk 601 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 486 optimal weight: 8.9990 overall best weight: 3.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN h 19 GLN E 36 HIS E 161 GLN E 209 HIS H 165 ASN I 52 ASN I 111 GLN ** J 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 GLN F 107 ASN K 32 HIS N 49 GLN M 28 HIS M 48 HIS P 103 ASN R 31 ASN T 10 ASN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 51 ASN g 64 HIS g 104 HIS ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 215 GLN j 18 HIS j 25 GLN z 183 ASN z 365 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 81718 Z= 0.326 Angle : 0.992 25.645 118136 Z= 0.499 Chirality : 0.044 0.629 14297 Planarity : 0.009 0.149 8884 Dihedral : 23.807 178.863 31524 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.53 % Allowed : 15.53 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.11), residues: 5088 helix: 0.12 (0.13), residues: 1694 sheet: -0.38 (0.16), residues: 909 loop : -0.93 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 64 HIS 0.014 0.001 HIS S 135 PHE 0.026 0.002 PHE C 236 TYR 0.016 0.002 TYR h 73 ARG 0.008 0.001 ARG O 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 774 time to evaluate : 4.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 187 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6569 (mtm110) REVERT: C 258 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7200 (mt-10) REVERT: D 143 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.6149 (tmt170) REVERT: F 188 TYR cc_start: 0.8012 (t80) cc_final: 0.7690 (t80) REVERT: L 8 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7472 (mtm180) REVERT: O 98 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7869 (tmt-80) REVERT: O 130 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6971 (tp30) REVERT: P 53 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7705 (mm110) REVERT: P 83 MET cc_start: 0.8262 (tpt) cc_final: 0.7711 (tpt) REVERT: Q 41 MET cc_start: 0.8655 (mmt) cc_final: 0.8370 (mmt) REVERT: T 83 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: V 51 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.7971 (mmmt) REVERT: Y 72 PHE cc_start: 0.8176 (m-80) cc_final: 0.7885 (t80) REVERT: Y 74 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7019 (mmt) REVERT: U 81 GLN cc_start: 0.8699 (pt0) cc_final: 0.8464 (pt0) REVERT: d 48 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7956 (tttt) REVERT: j 32 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7602 (ttm-80) REVERT: j 64 LYS cc_start: 0.7971 (pttm) cc_final: 0.7769 (ptmm) REVERT: z 160 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6741 (mm-40) REVERT: z 251 MET cc_start: 0.8136 (tpt) cc_final: 0.7906 (tpt) REVERT: z 277 MET cc_start: 0.8590 (ptt) cc_final: 0.8316 (ptt) REVERT: z 403 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6490 (mtm) outliers start: 158 outliers final: 71 residues processed: 858 average time/residue: 1.8585 time to fit residues: 2037.3684 Evaluate side-chains 833 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 749 time to evaluate : 4.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 193 LYS Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 53 GLN Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 107 LYS Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 83 GLN Chi-restraints excluded: chain V residue 51 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 37 LYS Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 99 GLU Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain U residue 44 LYS Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 32 ARG Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain z residue 160 GLN Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 215 LEU Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 403 MET Chi-restraints excluded: chain z residue 424 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 599 optimal weight: 5.9990 chunk 456 optimal weight: 8.9990 chunk 314 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 289 optimal weight: 20.0000 chunk 407 optimal weight: 0.7980 chunk 608 optimal weight: 5.9990 chunk 644 optimal weight: 2.9990 chunk 318 optimal weight: 0.9990 chunk 577 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 141 ASN h 19 GLN G 110 ASN ** G 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN I 111 GLN ** J 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 GLN F 107 ASN P 103 ASN R 31 ASN Y 19 GLN Y 22 GLN U 28 ASN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 56 ASN g 51 ASN g 64 HIS g 104 HIS ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 25 GLN j 60 ASN z 183 ASN z 309 GLN ** z 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 81718 Z= 0.228 Angle : 0.928 24.603 118136 Z= 0.475 Chirality : 0.040 0.343 14297 Planarity : 0.008 0.139 8884 Dihedral : 23.670 179.251 31524 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.26 % Allowed : 17.05 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.42 (0.11), residues: 5088 helix: 0.55 (0.13), residues: 1670 sheet: -0.21 (0.16), residues: 911 loop : -0.81 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 8 HIS 0.008 0.001 HIS S 135 PHE 0.017 0.002 PHE K 67 TYR 0.015 0.001 TYR R 84 ARG 0.008 0.000 ARG O 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 756 time to evaluate : 4.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 187 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6474 (mtm110) REVERT: E 168 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8076 (mmtm) REVERT: D 143 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.6408 (tmt90) REVERT: F 188 TYR cc_start: 0.7998 (t80) cc_final: 0.7691 (t80) REVERT: L 8 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7466 (mtm180) REVERT: L 146 THR cc_start: 0.8655 (m) cc_final: 0.8437 (m) REVERT: O 130 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6878 (tp30) REVERT: P 83 MET cc_start: 0.8248 (tpt) cc_final: 0.7877 (tpt) REVERT: Q 41 MET cc_start: 0.8630 (mmt) cc_final: 0.8238 (mmt) REVERT: T 83 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: Y 72 PHE cc_start: 0.8157 (m-80) cc_final: 0.7884 (t80) REVERT: Y 74 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7006 (mmt) REVERT: U 81 GLN cc_start: 0.8671 (pt0) cc_final: 0.8456 (pt0) REVERT: d 48 LYS cc_start: 0.8166 (ttmt) cc_final: 0.7923 (tttt) REVERT: g 113 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.5937 (t80) REVERT: z 160 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6445 (mm-40) REVERT: z 251 MET cc_start: 0.8084 (tpt) cc_final: 0.7846 (tpt) REVERT: z 277 MET cc_start: 0.8562 (ptt) cc_final: 0.8301 (ptt) REVERT: z 319 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6905 (mmt180) outliers start: 146 outliers final: 66 residues processed: 840 average time/residue: 1.9138 time to fit residues: 2049.2392 Evaluate side-chains 797 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 721 time to evaluate : 4.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 193 LYS Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain M residue 48 HIS Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain T residue 83 GLN Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 37 LYS Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 99 GLU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 44 LYS Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain g residue 42 MET Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 32 ARG Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain z residue 160 GLN Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 215 LEU Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 319 ARG Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 424 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 536 optimal weight: 4.9990 chunk 365 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 480 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 550 optimal weight: 9.9990 chunk 445 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 329 optimal weight: 10.0000 chunk 578 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 141 ASN B 95 ASN I 111 GLN J 75 ASN F 29 GLN F 107 ASN L 121 GLN P 103 ASN R 31 ASN Q 86 GLN ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 ASN S 42 HIS T 12 GLN Y 19 GLN Y 22 GLN U 28 ASN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 HIS g 104 HIS j 25 GLN z 183 ASN z 232 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 81718 Z= 0.380 Angle : 1.020 25.649 118136 Z= 0.510 Chirality : 0.045 0.420 14297 Planarity : 0.010 0.154 8884 Dihedral : 23.776 179.225 31522 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.31 % Allowed : 17.81 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.39 (0.11), residues: 5088 helix: 0.50 (0.13), residues: 1681 sheet: -0.14 (0.16), residues: 900 loop : -0.77 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 64 HIS 0.011 0.001 HIS S 135 PHE 0.026 0.002 PHE d 14 TYR 0.022 0.002 TYR T 65 ARG 0.010 0.001 ARG R 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 734 time to evaluate : 4.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 187 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6500 (mtm110) REVERT: C 258 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: C 263 LYS cc_start: 0.8601 (mtmt) cc_final: 0.8231 (ttpt) REVERT: E 168 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8106 (mmtm) REVERT: D 38 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6528 (mp0) REVERT: D 143 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6147 (tmt170) REVERT: D 150 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7340 (mtt) REVERT: D 157 MET cc_start: 0.8211 (tpp) cc_final: 0.7858 (tpt) REVERT: F 188 TYR cc_start: 0.8079 (t80) cc_final: 0.7791 (t80) REVERT: L 8 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7470 (mtm180) REVERT: O 97 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8099 (tt) REVERT: O 98 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7941 (tmt-80) REVERT: O 130 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6942 (tp30) REVERT: P 83 MET cc_start: 0.8275 (tpt) cc_final: 0.7849 (tpt) REVERT: Q 41 MET cc_start: 0.8596 (mmt) cc_final: 0.8320 (mmt) REVERT: S 69 THR cc_start: 0.8542 (m) cc_final: 0.8338 (m) REVERT: T 83 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: Y 72 PHE cc_start: 0.8201 (m-80) cc_final: 0.7888 (t80) REVERT: Y 74 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7055 (mmt) REVERT: U 81 GLN cc_start: 0.8698 (pt0) cc_final: 0.8496 (pt0) REVERT: d 48 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7906 (tttt) REVERT: z 160 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6783 (mm-40) REVERT: z 277 MET cc_start: 0.8593 (ptt) cc_final: 0.8309 (ptt) REVERT: z 319 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6921 (mmt180) outliers start: 148 outliers final: 81 residues processed: 829 average time/residue: 1.8764 time to fit residues: 1992.9794 Evaluate side-chains 813 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 718 time to evaluate : 4.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 193 LYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 83 GLN Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 44 LYS Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain g residue 42 MET Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 32 ARG Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain z residue 131 VAL Chi-restraints excluded: chain z residue 141 GLN Chi-restraints excluded: chain z residue 160 GLN Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 215 LEU Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 319 ARG Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 424 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 216 optimal weight: 2.9990 chunk 580 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 378 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 645 optimal weight: 2.9990 chunk 535 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 chunk 338 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 141 ASN h 19 GLN I 111 GLN F 29 GLN F 107 ASN L 121 GLN P 103 ASN R 31 ASN ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 10 ASN Y 19 GLN Y 22 GLN Y 85 ASN U 28 ASN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 56 ASN g 64 HIS j 25 GLN z 232 HIS ** z 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 81718 Z= 0.250 Angle : 0.936 24.603 118136 Z= 0.478 Chirality : 0.041 0.352 14297 Planarity : 0.009 0.140 8884 Dihedral : 23.616 179.847 31522 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.31 % Allowed : 18.82 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.20 (0.11), residues: 5088 helix: 0.75 (0.13), residues: 1677 sheet: -0.11 (0.16), residues: 919 loop : -0.69 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP d 8 HIS 0.007 0.001 HIS X 16 PHE 0.017 0.002 PHE K 67 TYR 0.018 0.001 TYR R 84 ARG 0.009 0.000 ARG I 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 734 time to evaluate : 4.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 187 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6500 (mtm110) REVERT: C 258 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: C 263 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8238 (ttpt) REVERT: E 168 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8017 (mmtm) REVERT: D 143 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.6089 (tmt170) REVERT: D 150 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7364 (mtt) REVERT: D 157 MET cc_start: 0.8207 (tpp) cc_final: 0.7875 (tpt) REVERT: F 188 TYR cc_start: 0.8024 (t80) cc_final: 0.7733 (t80) REVERT: L 8 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7454 (mtm180) REVERT: L 82 MET cc_start: 0.8371 (mtm) cc_final: 0.8154 (mtp) REVERT: O 98 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8061 (ttt-90) REVERT: O 130 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6898 (tp30) REVERT: P 83 MET cc_start: 0.8269 (tpt) cc_final: 0.7849 (tpt) REVERT: T 83 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: Y 72 PHE cc_start: 0.8185 (m-80) cc_final: 0.7893 (t80) REVERT: Y 74 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.6966 (mmt) REVERT: d 48 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7860 (tttt) REVERT: g 291 TRP cc_start: 0.6262 (OUTLIER) cc_final: 0.5604 (p90) REVERT: j 76 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7915 (pm20) REVERT: z 160 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6494 (mm-40) REVERT: z 250 GLU cc_start: 0.7793 (tt0) cc_final: 0.7553 (tt0) REVERT: z 277 MET cc_start: 0.8551 (ptt) cc_final: 0.8289 (ptt) REVERT: z 319 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6863 (mmt180) REVERT: z 344 GLN cc_start: 0.8126 (pm20) cc_final: 0.6953 (mt0) outliers start: 148 outliers final: 79 residues processed: 823 average time/residue: 1.8703 time to fit residues: 1966.6594 Evaluate side-chains 815 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 722 time to evaluate : 4.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain M residue 48 HIS Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 83 GLN Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 44 LYS Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain g residue 42 MET Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 32 ARG Chi-restraints excluded: chain j residue 76 GLU Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain z residue 141 GLN Chi-restraints excluded: chain z residue 160 GLN Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 215 LEU Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 319 ARG Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 424 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 622 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 367 optimal weight: 0.0870 chunk 471 optimal weight: 0.8980 chunk 365 optimal weight: 0.1980 chunk 543 optimal weight: 8.9990 chunk 360 optimal weight: 6.9990 chunk 642 optimal weight: 3.9990 chunk 402 optimal weight: 3.9990 chunk 391 optimal weight: 7.9990 chunk 296 optimal weight: 20.0000 overall best weight: 1.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 141 ASN E 188 ASN I 111 GLN ** J 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 GLN F 107 ASN L 121 GLN P 103 ASN P 137 HIS R 31 ASN S 72 GLN S 76 GLN Y 19 GLN Y 22 GLN U 28 ASN g 51 ASN g 64 HIS j 25 GLN z 232 HIS z 309 GLN ** z 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 81718 Z= 0.206 Angle : 0.912 24.143 118136 Z= 0.468 Chirality : 0.039 0.336 14297 Planarity : 0.008 0.137 8884 Dihedral : 23.525 179.141 31522 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.06 % Allowed : 19.31 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.02 (0.11), residues: 5088 helix: 0.92 (0.13), residues: 1693 sheet: 0.01 (0.16), residues: 912 loop : -0.61 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 45 HIS 0.005 0.001 HIS X 16 PHE 0.021 0.001 PHE H 192 TYR 0.021 0.001 TYR T 65 ARG 0.009 0.000 ARG O 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 742 time to evaluate : 4.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7152 (t0) REVERT: C 187 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6496 (mtm110) REVERT: C 258 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7210 (mt-10) REVERT: C 263 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8212 (ttpt) REVERT: h 36 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8723 (mp) REVERT: E 168 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8024 (mmtm) REVERT: D 143 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6303 (tmt90) REVERT: D 150 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7369 (mtt) REVERT: D 157 MET cc_start: 0.8185 (tpp) cc_final: 0.7886 (tpt) REVERT: F 188 TYR cc_start: 0.8006 (t80) cc_final: 0.7730 (t80) REVERT: L 8 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7451 (mtm180) REVERT: L 146 THR cc_start: 0.8693 (m) cc_final: 0.8432 (m) REVERT: O 98 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8002 (ttt-90) REVERT: O 130 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: P 83 MET cc_start: 0.8265 (tpt) cc_final: 0.7888 (tpt) REVERT: T 83 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: Y 72 PHE cc_start: 0.8163 (m-80) cc_final: 0.7892 (t80) REVERT: Y 74 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7004 (mmt) REVERT: d 48 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7892 (tttt) REVERT: g 113 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.6113 (t80) REVERT: g 291 TRP cc_start: 0.6218 (OUTLIER) cc_final: 0.5642 (p90) REVERT: j 76 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: z 160 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6405 (mm-40) REVERT: z 250 GLU cc_start: 0.7793 (tt0) cc_final: 0.7541 (tt0) REVERT: z 277 MET cc_start: 0.8524 (ptt) cc_final: 0.8266 (ptt) REVERT: z 319 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6884 (mmt180) REVERT: z 344 GLN cc_start: 0.8042 (pm20) cc_final: 0.6946 (mt0) outliers start: 137 outliers final: 75 residues processed: 832 average time/residue: 1.9023 time to fit residues: 2021.4819 Evaluate side-chains 812 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 720 time to evaluate : 4.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain G residue 25 ARG Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 83 GLN Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain Y residue 32 LYS Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 32 ARG Chi-restraints excluded: chain j residue 76 GLU Chi-restraints excluded: chain z residue 131 VAL Chi-restraints excluded: chain z residue 141 GLN Chi-restraints excluded: chain z residue 160 GLN Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 215 LEU Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 319 ARG Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 424 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 397 optimal weight: 9.9990 chunk 256 optimal weight: 7.9990 chunk 383 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 408 optimal weight: 5.9990 chunk 437 optimal weight: 1.9990 chunk 317 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 505 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN H 44 ASN I 111 GLN F 29 GLN L 121 GLN P 103 ASN R 31 ASN Q 24 HIS ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 GLN T 10 ASN Y 19 GLN Y 22 GLN U 28 ASN e 56 ASN g 64 HIS j 25 GLN z 232 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.140 81718 Z= 0.444 Angle : 1.054 25.900 118136 Z= 0.523 Chirality : 0.047 0.444 14297 Planarity : 0.010 0.156 8884 Dihedral : 23.740 179.177 31521 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 3.06 % Allowed : 19.62 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.21 (0.11), residues: 5088 helix: 0.67 (0.13), residues: 1686 sheet: -0.06 (0.16), residues: 911 loop : -0.67 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 30 HIS 0.012 0.001 HIS X 16 PHE 0.031 0.002 PHE d 14 TYR 0.022 0.002 TYR R 84 ARG 0.013 0.001 ARG H 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 721 time to evaluate : 5.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7099 (t0) REVERT: C 187 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6657 (mtm110) REVERT: C 258 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: h 36 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8722 (mp) REVERT: E 168 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8074 (mmtm) REVERT: D 143 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.6146 (tmt170) REVERT: D 150 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7335 (mtt) REVERT: D 157 MET cc_start: 0.8220 (tpp) cc_final: 0.7861 (tpt) REVERT: F 188 TYR cc_start: 0.8150 (t80) cc_final: 0.7906 (t80) REVERT: L 8 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7469 (mtm180) REVERT: O 97 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8146 (tt) REVERT: O 98 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7922 (tmt-80) REVERT: O 130 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: P 83 MET cc_start: 0.8287 (tpt) cc_final: 0.7902 (tpt) REVERT: T 83 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: Y 72 PHE cc_start: 0.8196 (m-80) cc_final: 0.7890 (t80) REVERT: Y 74 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7126 (mmt) REVERT: g 113 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6294 (t80) REVERT: g 291 TRP cc_start: 0.6454 (OUTLIER) cc_final: 0.5793 (p90) REVERT: j 76 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: z 160 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.6866 (mm-40) REVERT: z 231 ARG cc_start: 0.6188 (OUTLIER) cc_final: 0.5367 (mtm-85) REVERT: z 277 MET cc_start: 0.8620 (ptt) cc_final: 0.8335 (ptt) REVERT: z 319 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6868 (mmt180) REVERT: z 559 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5596 (pt0) outliers start: 137 outliers final: 76 residues processed: 804 average time/residue: 1.9088 time to fit residues: 1957.3363 Evaluate side-chains 803 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 707 time to evaluate : 4.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain G residue 25 ARG Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain P residue 137 HIS Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 83 GLN Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 32 ARG Chi-restraints excluded: chain j residue 76 GLU Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain z residue 131 VAL Chi-restraints excluded: chain z residue 141 GLN Chi-restraints excluded: chain z residue 160 GLN Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 215 LEU Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 319 ARG Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 424 VAL Chi-restraints excluded: chain z residue 559 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 584 optimal weight: 0.9980 chunk 615 optimal weight: 6.9990 chunk 561 optimal weight: 1.9990 chunk 599 optimal weight: 2.9990 chunk 360 optimal weight: 0.2980 chunk 260 optimal weight: 6.9990 chunk 470 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 541 optimal weight: 10.0000 chunk 566 optimal weight: 0.9980 chunk 596 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN I 111 GLN ** J 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 GLN F 179 ASN L 121 GLN P 103 ASN P 137 HIS R 31 ASN ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 GLN T 10 ASN T 128 GLN Y 19 GLN Y 22 GLN Y 85 ASN U 28 ASN g 64 HIS ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 25 GLN z 232 HIS z 309 GLN ** z 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 81718 Z= 0.160 Angle : 0.897 24.000 118136 Z= 0.463 Chirality : 0.038 0.322 14297 Planarity : 0.008 0.132 8884 Dihedral : 23.487 179.784 31521 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.17 % Allowed : 20.74 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.11 (0.12), residues: 5088 helix: 1.02 (0.13), residues: 1699 sheet: 0.05 (0.16), residues: 918 loop : -0.52 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 30 HIS 0.006 0.001 HIS z 273 PHE 0.014 0.001 PHE K 67 TYR 0.023 0.001 TYR R 84 ARG 0.014 0.000 ARG H 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 736 time to evaluate : 4.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 187 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6504 (mtm110) REVERT: E 168 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7998 (mmtm) REVERT: D 157 MET cc_start: 0.8127 (tpp) cc_final: 0.7830 (tpt) REVERT: F 188 TYR cc_start: 0.8007 (t80) cc_final: 0.7771 (t80) REVERT: L 8 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7433 (mtm180) REVERT: L 146 THR cc_start: 0.8656 (m) cc_final: 0.8393 (m) REVERT: O 130 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6968 (tp30) REVERT: P 83 MET cc_start: 0.8266 (tpt) cc_final: 0.7891 (tpt) REVERT: P 137 HIS cc_start: 0.5123 (OUTLIER) cc_final: 0.4905 (m-70) REVERT: S 108 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7733 (ttp-110) REVERT: T 83 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: Y 72 PHE cc_start: 0.8183 (m-80) cc_final: 0.7862 (t80) REVERT: Y 74 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.6980 (mmt) REVERT: d 48 LYS cc_start: 0.8135 (ttmt) cc_final: 0.7929 (tttt) REVERT: g 291 TRP cc_start: 0.6312 (OUTLIER) cc_final: 0.5874 (p90) REVERT: j 76 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: z 160 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6255 (mm-40) REVERT: z 250 GLU cc_start: 0.7894 (tt0) cc_final: 0.7651 (tt0) REVERT: z 277 MET cc_start: 0.8499 (ptt) cc_final: 0.8246 (ptt) REVERT: z 319 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6842 (mmt180) REVERT: z 344 GLN cc_start: 0.7962 (pm20) cc_final: 0.6901 (mt0) REVERT: z 395 MET cc_start: 0.6517 (ttp) cc_final: 0.6086 (ttp) outliers start: 97 outliers final: 56 residues processed: 798 average time/residue: 1.9035 time to fit residues: 1946.7280 Evaluate side-chains 787 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 720 time to evaluate : 4.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain G residue 25 ARG Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 137 HIS Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 83 GLN Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain j residue 32 ARG Chi-restraints excluded: chain j residue 76 GLU Chi-restraints excluded: chain z residue 131 VAL Chi-restraints excluded: chain z residue 160 GLN Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 319 ARG Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 424 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 393 optimal weight: 7.9990 chunk 633 optimal weight: 2.9990 chunk 386 optimal weight: 0.1980 chunk 300 optimal weight: 10.0000 chunk 440 optimal weight: 0.1980 chunk 664 optimal weight: 20.0000 chunk 611 optimal weight: 9.9990 chunk 529 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 408 optimal weight: 5.9990 chunk 324 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN I 111 GLN F 29 GLN L 121 GLN P 103 ASN P 137 HIS R 31 ASN ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 GLN Y 19 GLN Y 22 GLN Y 85 ASN U 28 ASN e 56 ASN g 64 HIS ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 232 HIS z 309 GLN ** z 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 81718 Z= 0.242 Angle : 0.935 24.146 118136 Z= 0.476 Chirality : 0.040 0.347 14297 Planarity : 0.009 0.140 8884 Dihedral : 23.515 179.255 31521 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.92 % Allowed : 21.05 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.13 (0.12), residues: 5088 helix: 1.05 (0.13), residues: 1683 sheet: 0.05 (0.16), residues: 925 loop : -0.51 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 30 HIS 0.014 0.001 HIS P 137 PHE 0.018 0.002 PHE P 141 TYR 0.023 0.001 TYR R 84 ARG 0.015 0.000 ARG H 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 726 time to evaluate : 4.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 187 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6496 (mtm110) REVERT: E 168 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8028 (mmtm) REVERT: D 157 MET cc_start: 0.8181 (tpp) cc_final: 0.7866 (tpt) REVERT: F 188 TYR cc_start: 0.8088 (t80) cc_final: 0.7826 (t80) REVERT: L 8 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7453 (mtm180) REVERT: O 97 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.7975 (tt) REVERT: O 98 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7972 (ttt-90) REVERT: O 130 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6894 (tp30) REVERT: P 83 MET cc_start: 0.8264 (tpt) cc_final: 0.7880 (tpt) REVERT: S 108 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7734 (ttp-110) REVERT: T 83 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: Y 72 PHE cc_start: 0.8179 (m-80) cc_final: 0.7904 (t80) REVERT: Y 74 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7046 (mmt) REVERT: d 48 LYS cc_start: 0.8116 (ttmt) cc_final: 0.7888 (tttt) REVERT: g 291 TRP cc_start: 0.6443 (OUTLIER) cc_final: 0.5963 (p90) REVERT: j 76 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: z 160 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6442 (mm-40) REVERT: z 231 ARG cc_start: 0.6181 (OUTLIER) cc_final: 0.5361 (mtm-85) REVERT: z 250 GLU cc_start: 0.7844 (tt0) cc_final: 0.7604 (tt0) REVERT: z 277 MET cc_start: 0.8534 (ptt) cc_final: 0.8268 (ptt) REVERT: z 319 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6848 (mmt180) REVERT: z 344 GLN cc_start: 0.8161 (pm20) cc_final: 0.7019 (mt0) outliers start: 86 outliers final: 61 residues processed: 784 average time/residue: 1.9132 time to fit residues: 1906.7621 Evaluate side-chains 790 residues out of total 4508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 716 time to evaluate : 4.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain G residue 25 ARG Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 83 GLN Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 291 TRP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain j residue 32 ARG Chi-restraints excluded: chain j residue 76 GLU Chi-restraints excluded: chain z residue 131 VAL Chi-restraints excluded: chain z residue 160 GLN Chi-restraints excluded: chain z residue 201 ASN Chi-restraints excluded: chain z residue 231 ARG Chi-restraints excluded: chain z residue 319 ARG Chi-restraints excluded: chain z residue 346 VAL Chi-restraints excluded: chain z residue 424 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 420 optimal weight: 3.9990 chunk 563 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 487 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 529 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 544 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN I 111 GLN F 29 GLN F 179 ASN L 121 GLN P 103 ASN P 137 HIS R 31 ASN ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 10 ASN T 128 GLN Y 19 GLN Y 22 GLN Y 85 ASN U 28 ASN g 64 HIS ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 25 GLN z 232 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.163317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.142455 restraints weight = 75367.359| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 0.87 r_work: 0.3302 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 81718 Z= 0.379 Angle : 1.014 25.163 118136 Z= 0.507 Chirality : 0.045 0.408 14297 Planarity : 0.009 0.152 8884 Dihedral : 23.649 179.198 31521 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.08 % Allowed : 21.23 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.01 (0.11), residues: 5088 helix: 0.90 (0.13), residues: 1671 sheet: -0.00 (0.16), residues: 921 loop : -0.57 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 30 HIS 0.011 0.001 HIS X 16 PHE 0.026 0.002 PHE d 14 TYR 0.027 0.002 TYR z 234 ARG 0.015 0.001 ARG H 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26960.14 seconds wall clock time: 468 minutes 56.03 seconds (28136.03 seconds total)