Starting phenix.real_space_refine on Sun Mar 24 12:19:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7p_0360/03_2024/6n7p_0360.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7p_0360/03_2024/6n7p_0360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7p_0360/03_2024/6n7p_0360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7p_0360/03_2024/6n7p_0360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7p_0360/03_2024/6n7p_0360.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7p_0360/03_2024/6n7p_0360.pdb" } resolution = 3.6 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 580 5.49 5 S 93 5.16 5 C 23851 2.51 5 N 7348 2.21 5 O 9613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D ARG 365": "NH1" <-> "NH2" Residue "D ARG 406": "NH1" <-> "NH2" Residue "D ARG 484": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "E ARG 334": "NH1" <-> "NH2" Residue "E ARG 341": "NH1" <-> "NH2" Residue "E ARG 492": "NH1" <-> "NH2" Residue "E ARG 580": "NH1" <-> "NH2" Residue "F TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 358": "NH1" <-> "NH2" Residue "F ARG 377": "NH1" <-> "NH2" Residue "F ARG 379": "NH1" <-> "NH2" Residue "F TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "G PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 138": "NH1" <-> "NH2" Residue "G PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 271": "NH1" <-> "NH2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "I ASP 41": "OD1" <-> "OD2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "I ARG 103": "NH1" <-> "NH2" Residue "I ARG 233": "NH1" <-> "NH2" Residue "K ARG 62": "NH1" <-> "NH2" Residue "K ARG 126": "NH1" <-> "NH2" Residue "L ARG 88": "NH1" <-> "NH2" Residue "L ARG 117": "NH1" <-> "NH2" Residue "M ARG 8": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 89": "NH1" <-> "NH2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "N PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 90": "NH1" <-> "NH2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "P ARG 26": "NH1" <-> "NH2" Residue "P TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "Q ARG 23": "NH1" <-> "NH2" Residue "Q ARG 30": "NH1" <-> "NH2" Residue "Q TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 75": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41488 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1207 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 14, 'TRANS': 171} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 7, 'TYR:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 6, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 185 Chain: "B" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1570 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 186} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1058 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4561 Classifications: {'peptide': 544} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 531} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 3981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 3981 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 236} Link IDs: {'PTRANS': 19, 'TRANS': 556} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 942 Unresolved non-hydrogen angles: 1218 Unresolved non-hydrogen dihedrals: 808 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 19, 'TRP:plan': 9, 'ASP:plan': 14, 'PHE:plan': 18, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 552 Chain: "F" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1818 Classifications: {'peptide': 267} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 253} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 137 Chain: "G" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1954 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 685 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'UNK:plan-1': 53} Unresolved non-hydrogen planarities: 53 Chain: "I" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1409 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "J" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 984 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 185} Link IDs: {'PTRANS': 6, 'TRANS': 191} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 719 Unresolved non-hydrogen angles: 909 Unresolved non-hydrogen dihedrals: 604 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 20, 'PHE:plan': 10, 'GLU:plan': 16, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 427 Chain: "K" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1008 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 113} 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: "M" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 858 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 710 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 85} 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: "O" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "P" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 584 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Q" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 543 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 11822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 11822 Classifications: {'RNA': 558} Modifications used: {'rna2p_pur': 24, 'rna2p_pyr': 35, 'rna3p_pur': 241, 'rna3p_pyr': 258} Link IDs: {'rna2p': 59, 'rna3p': 498} Chain breaks: 1 Chain: "r" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 471 Classifications: {'RNA': 22} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 19} Chain: "X" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 826, 4101 Classifications: {'peptide': 826} Incomplete info: {'truncation_to_alanine': 754} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 27, 'TRANS': 793} Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 2812 Unresolved non-hydrogen angles: 3630 Unresolved non-hydrogen dihedrals: 2338 Unresolved non-hydrogen chiralities: 252 Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 8, 'TYR:plan': 35, 'ASN:plan1': 68, 'TRP:plan': 11, 'ASP:plan': 49, 'PHE:plan': 58, 'GLU:plan': 73, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 1621 Chain: "Y" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 677 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 5, 'TRANS': 132} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 447 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 376 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 11, 'PHE:plan': 11, 'GLU:plan': 9, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 260 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1248 SG CYS B 6 120.136 144.976 97.700 1.00 27.17 S ATOM 1275 SG CYS B 9 118.651 142.217 100.534 1.00 25.43 S ATOM 17019 SG CYS I 45 152.320 157.333 120.894 1.00 84.64 S ATOM 17076 SG CYS I 53 149.669 154.790 119.783 1.00 77.17 S ATOM 17182 SG CYS I 68 148.399 157.764 120.616 1.00 89.42 S ATOM 17882 SG CYS I 201 142.303 134.067 118.473 1.00 73.68 S ATOM 17904 SG CYS I 204 141.052 136.818 119.134 1.00 72.15 S Time building chain proxies: 22.53, per 1000 atoms: 0.54 Number of scatterers: 41488 At special positions: 0 Unit cell: (201.28, 272, 213.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 93 16.00 P 580 15.00 O 9613 8.00 N 7348 7.00 C 23851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.53 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 30 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 24 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 6 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 9 " pdb=" ZN I 501 " pdb="ZN ZN I 501 " - pdb=" NE2 HIS I 72 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 53 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 68 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 45 " pdb=" ZN I 502 " pdb="ZN ZN I 502 " - pdb=" ND1 HIS I 226 " pdb="ZN ZN I 502 " - pdb=" NE2 HIS I 220 " pdb="ZN ZN I 502 " - pdb=" SG CYS I 204 " pdb="ZN ZN I 502 " - pdb=" SG CYS I 201 " Number of angles added : 7 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8180 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 26 sheets defined 55.4% alpha, 8.7% beta 179 base pairs and 331 stacking pairs defined. Time for finding SS restraints: 13.59 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 removed outlier: 3.506A pdb=" N ARG A 14 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 57 Processing helix chain 'A' and resid 65 through 91 removed outlier: 3.615A pdb=" N ASN A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.569A pdb=" N ALA A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 26 removed outlier: 3.784A pdb=" N SER B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 48 Processing helix chain 'B' and resid 60 through 69 Processing helix chain 'B' and resid 79 through 100 Processing helix chain 'B' and resid 103 through 109 removed outlier: 3.889A pdb=" N LEU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.607A pdb=" N VAL B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.860A pdb=" N SER B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 28 removed outlier: 3.529A pdb=" N TYR C 19 " --> pdb=" O ASN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 removed outlier: 3.737A pdb=" N ASN C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 removed outlier: 3.578A pdb=" N ALA C 87 " --> pdb=" O THR C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 Processing helix chain 'C' and resid 134 through 148 Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 23 removed outlier: 4.469A pdb=" N SER D 14 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR D 15 " --> pdb=" O GLU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 40 removed outlier: 4.047A pdb=" N TRP D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 67 removed outlier: 3.838A pdb=" N LEU D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 removed outlier: 3.745A pdb=" N TYR D 74 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 101 removed outlier: 3.814A pdb=" N SER D 90 " --> pdb=" O ASN D 86 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS D 92 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 3.557A pdb=" N TRP D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL D 119 " --> pdb=" O PHE D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 138 Processing helix chain 'D' and resid 143 through 158 Processing helix chain 'D' and resid 162 through 173 removed outlier: 3.914A pdb=" N GLU D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 192 removed outlier: 3.912A pdb=" N TRP D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 202 removed outlier: 3.674A pdb=" N SER D 200 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 202 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 Processing helix chain 'D' and resid 222 through 255 removed outlier: 3.524A pdb=" N LEU D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 290 removed outlier: 3.576A pdb=" N ILE D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR D 288 " --> pdb=" O ASP D 284 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 289 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 303 Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.613A pdb=" N ILE D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 341 removed outlier: 3.688A pdb=" N LEU D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 358 removed outlier: 3.647A pdb=" N SER D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 375 removed outlier: 3.577A pdb=" N LEU D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 369 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 370 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 382 Processing helix chain 'D' and resid 384 through 403 removed outlier: 3.951A pdb=" N PHE D 388 " --> pdb=" O ASP D 384 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP D 390 " --> pdb=" O GLU D 386 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE D 394 " --> pdb=" O ASP D 390 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR D 403 " --> pdb=" O GLN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 429 removed outlier: 4.063A pdb=" N LYS D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 427 " --> pdb=" O LYS D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 443 Processing helix chain 'D' and resid 450 through 460 Processing helix chain 'D' and resid 460 through 468 Processing helix chain 'D' and resid 469 through 475 Processing helix chain 'D' and resid 475 through 488 removed outlier: 3.933A pdb=" N TRP D 479 " --> pdb=" O ASN D 475 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE D 486 " --> pdb=" O TYR D 482 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 488 " --> pdb=" O ARG D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 505 Processing helix chain 'D' and resid 506 through 509 removed outlier: 3.698A pdb=" N ILE D 509 " --> pdb=" O TRP D 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 506 through 509' Processing helix chain 'D' and resid 510 through 512 No H-bonds generated for 'chain 'D' and resid 510 through 512' Processing helix chain 'D' and resid 513 through 529 Proline residue: D 519 - end of helix removed outlier: 3.940A pdb=" N GLU D 523 " --> pdb=" O PRO D 519 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE D 524 " --> pdb=" O SER D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 3.673A pdb=" N LEU D 536 " --> pdb=" O GLU D 532 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 63 removed outlier: 3.595A pdb=" N LEU E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 84 Processing helix chain 'E' and resid 87 through 101 removed outlier: 4.100A pdb=" N SER E 93 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE E 94 " --> pdb=" O PRO E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 118 removed outlier: 3.509A pdb=" N TYR E 109 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Proline residue: E 110 - end of helix removed outlier: 3.500A pdb=" N PHE E 113 " --> pdb=" O TYR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 138 through 152 Proline residue: E 144 - end of helix Processing helix chain 'E' and resid 160 through 174 removed outlier: 3.692A pdb=" N GLU E 164 " --> pdb=" O ASN E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 190 Proline residue: E 187 - end of helix removed outlier: 3.579A pdb=" N ASP E 190 " --> pdb=" O HIS E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 206 removed outlier: 3.732A pdb=" N GLN E 206 " --> pdb=" O TRP E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 240 removed outlier: 3.905A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 252 removed outlier: 3.753A pdb=" N THR E 251 " --> pdb=" O ARG E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 265 Processing helix chain 'E' and resid 270 through 285 removed outlier: 3.766A pdb=" N LEU E 285 " --> pdb=" O TRP E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 304 removed outlier: 3.576A pdb=" N TRP E 293 " --> pdb=" O HIS E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 321 removed outlier: 3.974A pdb=" N VAL E 310 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 339 Processing helix chain 'E' and resid 340 through 342 No H-bonds generated for 'chain 'E' and resid 340 through 342' Processing helix chain 'E' and resid 344 through 362 removed outlier: 3.541A pdb=" N ASN E 348 " --> pdb=" O ASN E 344 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN E 349 " --> pdb=" O THR E 345 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE E 361 " --> pdb=" O ARG E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 380 Processing helix chain 'E' and resid 388 through 412 removed outlier: 3.578A pdb=" N ILE E 392 " --> pdb=" O SER E 388 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN E 412 " --> pdb=" O THR E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 425 removed outlier: 3.777A pdb=" N THR E 423 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 444 removed outlier: 3.939A pdb=" N VAL E 433 " --> pdb=" O ASN E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 459 Processing helix chain 'E' and resid 467 through 481 removed outlier: 3.553A pdb=" N TRP E 471 " --> pdb=" O SER E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 492 Processing helix chain 'E' and resid 501 through 520 removed outlier: 3.598A pdb=" N THR E 518 " --> pdb=" O THR E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 529 removed outlier: 3.790A pdb=" N SER E 527 " --> pdb=" O VAL E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 544 Processing helix chain 'E' and resid 561 through 565 removed outlier: 3.795A pdb=" N LYS E 564 " --> pdb=" O ASP E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 625 removed outlier: 3.544A pdb=" N GLU E 622 " --> pdb=" O ASP E 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 184 Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.528A pdb=" N GLU F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 334 removed outlier: 3.578A pdb=" N TYR F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE F 333 " --> pdb=" O LEU F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 368 Processing helix chain 'F' and resid 386 through 398 Processing helix chain 'F' and resid 500 through 519 removed outlier: 3.880A pdb=" N ASN F 504 " --> pdb=" O GLU F 500 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN F 518 " --> pdb=" O GLU F 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 57 removed outlier: 3.507A pdb=" N ASN G 50 " --> pdb=" O ASP G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 93 removed outlier: 3.906A pdb=" N PHE G 82 " --> pdb=" O ASP G 78 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS G 85 " --> pdb=" O GLN G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 142 removed outlier: 4.122A pdb=" N LYS G 137 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU G 139 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N TRP G 140 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 222 removed outlier: 4.026A pdb=" N GLN G 221 " --> pdb=" O ASN G 217 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL G 222 " --> pdb=" O PHE G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 251 Processing helix chain 'G' and resid 262 through 270 removed outlier: 4.059A pdb=" N SER G 268 " --> pdb=" O LYS G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 293 Processing helix chain 'H' and resid 8 through 14 removed outlier: 3.649A pdb=" N TYR H 12 " --> pdb=" O SER H 8 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER H 14 " --> pdb=" O GLN H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 41 Processing helix chain 'H' and resid 43 through 52 Processing helix chain 'H' and resid 1268 through 1272 removed outlier: 3.969A pdb=" N UNK H1271 " --> pdb=" O UNK H1268 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N UNK H1272 " --> pdb=" O UNK H1269 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1268 through 1272' Processing helix chain 'H' and resid 1277 through 1314 removed outlier: 3.715A pdb=" N UNK H1281 " --> pdb=" O UNK H1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 19 removed outlier: 3.555A pdb=" N GLU I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 51 Processing helix chain 'I' and resid 73 through 86 Processing helix chain 'I' and resid 90 through 124 removed outlier: 3.792A pdb=" N GLU I 94 " --> pdb=" O PHE I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 138 Processing helix chain 'I' and resid 173 through 196 removed outlier: 3.512A pdb=" N GLN I 196 " --> pdb=" O GLN I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 222 removed outlier: 3.657A pdb=" N LEU I 217 " --> pdb=" O THR I 213 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU I 222 " --> pdb=" O ALA I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 244 Processing helix chain 'J' and resid 356 through 369 Processing helix chain 'J' and resid 378 through 387 Proline residue: J 384 - end of helix Processing helix chain 'J' and resid 389 through 397 removed outlier: 3.672A pdb=" N LEU J 393 " --> pdb=" O ASP J 389 " (cutoff:3.500A) Processing helix chain 'J' and resid 399 through 431 Processing helix chain 'J' and resid 441 through 443 No H-bonds generated for 'chain 'J' and resid 441 through 443' Processing helix chain 'J' and resid 444 through 454 Processing helix chain 'J' and resid 463 through 508 removed outlier: 4.118A pdb=" N ILE J 467 " --> pdb=" O ASP J 463 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER J 468 " --> pdb=" O LYS J 464 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU J 469 " --> pdb=" O GLU J 465 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE J 492 " --> pdb=" O ASN J 488 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU J 493 " --> pdb=" O GLU J 489 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN J 495 " --> pdb=" O ARG J 491 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS J 496 " --> pdb=" O ILE J 492 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS J 498 " --> pdb=" O GLU J 494 " (cutoff:3.500A) Processing helix chain 'J' and resid 518 through 527 removed outlier: 3.759A pdb=" N GLU J 525 " --> pdb=" O LEU J 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 548 Processing helix chain 'K' and resid 56 through 62 removed outlier: 3.812A pdb=" N ASP K 59 " --> pdb=" O THR K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 131 Processing helix chain 'L' and resid 3 through 8 removed outlier: 3.622A pdb=" N LEU L 7 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 68 Processing helix chain 'L' and resid 102 through 107 Processing helix chain 'L' and resid 109 through 118 Processing helix chain 'M' and resid 3 through 8 removed outlier: 3.909A pdb=" N ARG M 8 " --> pdb=" O GLN M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 13 removed outlier: 3.658A pdb=" N LEU M 13 " --> pdb=" O LYS M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 28 Processing helix chain 'M' and resid 31 through 40 Processing helix chain 'N' and resid 4 through 14 removed outlier: 4.627A pdb=" N VAL N 8 " --> pdb=" O ASN N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 67 No H-bonds generated for 'chain 'N' and resid 65 through 67' Processing helix chain 'N' and resid 76 through 85 Proline residue: N 82 - end of helix Processing helix chain 'O' and resid 12 through 23 Processing helix chain 'P' and resid 14 through 22 Processing helix chain 'X' and resid 38 through 44 Processing helix chain 'X' and resid 52 through 68 Processing helix chain 'X' and resid 74 through 86 removed outlier: 3.614A pdb=" N SER X 80 " --> pdb=" O ASN X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 89 through 91 No H-bonds generated for 'chain 'X' and resid 89 through 91' Processing helix chain 'X' and resid 92 through 107 removed outlier: 3.549A pdb=" N LEU X 99 " --> pdb=" O ALA X 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 107 through 128 Processing helix chain 'X' and resid 129 through 131 No H-bonds generated for 'chain 'X' and resid 129 through 131' Processing helix chain 'X' and resid 132 through 137 Processing helix chain 'X' and resid 144 through 157 Processing helix chain 'X' and resid 162 through 175 Processing helix chain 'X' and resid 188 through 203 removed outlier: 3.541A pdb=" N THR X 199 " --> pdb=" O ILE X 195 " (cutoff:3.500A) Processing helix chain 'X' and resid 212 through 234 removed outlier: 4.007A pdb=" N LEU X 232 " --> pdb=" O GLU X 228 " (cutoff:3.500A) Processing helix chain 'X' and resid 235 through 242 removed outlier: 3.949A pdb=" N ASN X 239 " --> pdb=" O THR X 235 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU X 240 " --> pdb=" O THR X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 269 removed outlier: 3.631A pdb=" N LEU X 260 " --> pdb=" O VAL X 256 " (cutoff:3.500A) Proline residue: X 261 - end of helix Processing helix chain 'X' and resid 294 through 299 removed outlier: 3.525A pdb=" N THR X 299 " --> pdb=" O ASN X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 349 through 367 removed outlier: 3.511A pdb=" N SER X 365 " --> pdb=" O ASP X 361 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU X 366 " --> pdb=" O LEU X 362 " (cutoff:3.500A) Processing helix chain 'X' and resid 369 through 378 removed outlier: 3.723A pdb=" N ARG X 375 " --> pdb=" O LYS X 371 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN X 376 " --> pdb=" O GLU X 372 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE X 378 " --> pdb=" O ALA X 374 " (cutoff:3.500A) Processing helix chain 'X' and resid 413 through 427 removed outlier: 3.874A pdb=" N LEU X 417 " --> pdb=" O LYS X 413 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE X 419 " --> pdb=" O GLU X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 435 through 449 removed outlier: 3.773A pdb=" N PHE X 439 " --> pdb=" O PRO X 435 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR X 440 " --> pdb=" O PHE X 436 " (cutoff:3.500A) Processing helix chain 'X' and resid 453 through 468 Processing helix chain 'X' and resid 469 through 472 Processing helix chain 'X' and resid 473 through 489 Processing helix chain 'X' and resid 496 through 499 Processing helix chain 'X' and resid 500 through 505 removed outlier: 3.507A pdb=" N SER X 504 " --> pdb=" O TRP X 500 " (cutoff:3.500A) Processing helix chain 'X' and resid 513 through 531 removed outlier: 3.504A pdb=" N LEU X 529 " --> pdb=" O LYS X 525 " (cutoff:3.500A) Processing helix chain 'X' and resid 532 through 540 removed outlier: 3.534A pdb=" N VAL X 536 " --> pdb=" O ASN X 532 " (cutoff:3.500A) Processing helix chain 'X' and resid 543 through 548 removed outlier: 3.541A pdb=" N LYS X 546 " --> pdb=" O GLU X 543 " (cutoff:3.500A) Processing helix chain 'X' and resid 563 through 568 Processing helix chain 'X' and resid 590 through 600 Processing helix chain 'X' and resid 606 through 623 removed outlier: 3.606A pdb=" N ILE X 616 " --> pdb=" O GLU X 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU X 617 " --> pdb=" O LEU X 613 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU X 623 " --> pdb=" O GLU X 619 " (cutoff:3.500A) Processing helix chain 'X' and resid 632 through 647 Processing helix chain 'X' and resid 650 through 661 Processing helix chain 'X' and resid 661 through 668 Processing helix chain 'X' and resid 675 through 691 removed outlier: 3.870A pdb=" N LYS X 679 " --> pdb=" O ASP X 675 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE X 682 " --> pdb=" O THR X 678 " (cutoff:3.500A) Processing helix chain 'X' and resid 694 through 708 removed outlier: 3.538A pdb=" N LEU X 700 " --> pdb=" O GLN X 696 " (cutoff:3.500A) Processing helix chain 'X' and resid 712 through 720 Processing helix chain 'X' and resid 724 through 728 removed outlier: 3.953A pdb=" N LYS X 727 " --> pdb=" O THR X 724 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN X 728 " --> pdb=" O GLY X 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 724 through 728' Processing helix chain 'X' and resid 733 through 764 Processing helix chain 'X' and resid 771 through 781 Processing helix chain 'X' and resid 811 through 821 Processing helix chain 'X' and resid 823 through 830 Processing helix chain 'X' and resid 830 through 836 Processing helix chain 'X' and resid 848 through 860 removed outlier: 3.952A pdb=" N TRP X 854 " --> pdb=" O THR X 850 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE X 855 " --> pdb=" O ILE X 851 " (cutoff:3.500A) Processing helix chain 'Y' and resid 34 through 40 Processing helix chain 'Y' and resid 58 through 67 Processing helix chain 'Y' and resid 68 through 70 No H-bonds generated for 'chain 'Y' and resid 68 through 70' Processing helix chain 'Y' and resid 96 through 107 Processing helix chain 'Y' and resid 150 through 153 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 140 removed outlier: 6.644A pdb=" N VAL A 154 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE A 136 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE A 152 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE A 138 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N TYR A 150 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS A 140 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LYS A 148 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 176 Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.891A pdb=" N TYR B 4 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER B 11 " --> pdb=" O CYS B 6 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AA5, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'E' and resid 576 through 577 Processing sheet with id=AA8, first strand: chain 'E' and resid 582 through 583 Processing sheet with id=AA9, first strand: chain 'F' and resid 163 through 167 removed outlier: 4.920A pdb=" N TYR F 207 " --> pdb=" O VAL F 196 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AB2, first strand: chain 'F' and resid 339 through 341 removed outlier: 3.627A pdb=" N TYR F 341 " --> pdb=" O GLN F 354 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 444 through 446 Processing sheet with id=AB4, first strand: chain 'G' and resid 69 through 76 removed outlier: 3.527A pdb=" N THR G 76 " --> pdb=" O MET G 111 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET G 111 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 157 through 164 removed outlier: 5.841A pdb=" N LEU G 157 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY G 159 " --> pdb=" O VAL G 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 167 through 168 Processing sheet with id=AB7, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AB8, first strand: chain 'I' and resid 199 through 200 Processing sheet with id=AB9, first strand: chain 'K' and resid 80 through 81 removed outlier: 3.507A pdb=" N ILE K 31 " --> pdb=" O ILE K 49 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG K 21 " --> pdb=" O VAL K 97 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL K 97 " --> pdb=" O ARG K 21 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU K 23 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N THR K 95 " --> pdb=" O LEU K 23 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL K 97 " --> pdb=" O TYR L 84 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N TYR L 84 " --> pdb=" O VAL K 97 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR L 41 " --> pdb=" O TYR L 84 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN L 86 " --> pdb=" O ILE L 39 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE L 39 " --> pdb=" O ASN L 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 80 through 81 removed outlier: 3.507A pdb=" N ILE K 31 " --> pdb=" O ILE K 49 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL K 44 " --> pdb=" O MET K 35 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU N 22 " --> pdb=" O LYS N 70 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE N 72 " --> pdb=" O SER N 20 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N SER N 20 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 24 through 28 removed outlier: 6.290A pdb=" N THR L 16 " --> pdb=" O ILE L 95 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE L 95 " --> pdb=" O THR L 16 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU L 18 " --> pdb=" O ARG L 93 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN M 83 " --> pdb=" O LYS M 80 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS M 93 " --> pdb=" O GLU M 70 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU M 70 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE M 95 " --> pdb=" O VAL M 68 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL M 68 " --> pdb=" O PHE M 95 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU M 69 " --> pdb=" O LYS M 59 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS M 59 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASN M 71 " --> pdb=" O ARG M 57 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG M 57 " --> pdb=" O ASN M 71 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL M 103 " --> pdb=" O SER M 47 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU P 70 " --> pdb=" O LYS M 106 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN P 52 " --> pdb=" O SER P 44 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER P 44 " --> pdb=" O GLN P 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AC4, first strand: chain 'N' and resid 43 through 50 removed outlier: 7.326A pdb=" N ASP N 60 " --> pdb=" O ASP N 46 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE N 48 " --> pdb=" O HIS N 58 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N HIS N 58 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR N 50 " --> pdb=" O VAL N 56 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL N 56 " --> pdb=" O THR N 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 76 through 78 removed outlier: 6.059A pdb=" N ALA O 57 " --> pdb=" O LEU O 77 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS P 30 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE P 81 " --> pdb=" O GLY P 28 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY P 28 " --> pdb=" O ILE P 81 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLU P 83 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ARG P 26 " --> pdb=" O GLU P 83 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 76 through 78 removed outlier: 6.059A pdb=" N ALA O 57 " --> pdb=" O LEU O 77 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL O 53 " --> pdb=" O VAL O 44 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS O 42 " --> pdb=" O ASP O 55 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA O 57 " --> pdb=" O LYS O 40 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS O 40 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU O 59 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG O 38 " --> pdb=" O GLU O 59 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU O 89 " --> pdb=" O TRP O 30 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS Q 55 " --> pdb=" O GLU Q 45 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ALA Q 43 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU Q 59 " --> pdb=" O ASP Q 41 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP Q 41 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR Q 61 " --> pdb=" O VAL Q 39 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL Q 39 " --> pdb=" O THR Q 61 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL Q 39 " --> pdb=" O ARG Q 30 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA Q 43 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA Q 26 " --> pdb=" O ALA Q 43 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER Q 70 " --> pdb=" O ASN Q 18 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Y' and resid 47 through 51 removed outlier: 4.466A pdb=" N PHE Y 89 " --> pdb=" O GLY Y 78 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 148 through 149 1653 hydrogen bonds defined for protein. 4788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 428 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 179 basepair parallelities 331 stacking parallelities Total time for adding SS restraints: 21.17 Time building geometry restraints manager: 18.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5954 1.31 - 1.44: 14259 1.44 - 1.56: 21797 1.56 - 1.69: 1158 1.69 - 1.81: 152 Bond restraints: 43320 Sorted by residual: bond pdb=" CA HIS A 99 " pdb=" C HIS A 99 " ideal model delta sigma weight residual 1.523 1.587 -0.064 1.34e-02 5.57e+03 2.28e+01 bond pdb=" CG1 ILE D 171 " pdb=" CD1 ILE D 171 " ideal model delta sigma weight residual 1.513 1.363 0.150 3.90e-02 6.57e+02 1.49e+01 bond pdb=" N SER D 266 " pdb=" CA SER D 266 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.46e+01 bond pdb=" N VAL D 445 " pdb=" CA VAL D 445 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.09e-02 8.42e+03 1.12e+01 bond pdb=" N ASN X 282 " pdb=" CA ASN X 282 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.04e+01 ... (remaining 43315 not shown) Histogram of bond angle deviations from ideal: 82.18 - 94.87: 2 94.87 - 107.56: 5312 107.56 - 120.25: 39454 120.25 - 132.94: 16852 132.94 - 145.63: 58 Bond angle restraints: 61678 Sorted by residual: angle pdb=" N TRP X 281 " pdb=" CA TRP X 281 " pdb=" C TRP X 281 " ideal model delta sigma weight residual 110.61 121.80 -11.19 1.25e+00 6.40e-01 8.01e+01 angle pdb=" C GLU X 673 " pdb=" N LEU X 674 " pdb=" CA LEU X 674 " ideal model delta sigma weight residual 121.54 138.02 -16.48 1.91e+00 2.74e-01 7.45e+01 angle pdb=" O3' U R 442 " pdb=" P U R 443 " pdb=" OP2 U R 443 " ideal model delta sigma weight residual 108.00 82.18 25.82 3.00e+00 1.11e-01 7.41e+01 angle pdb=" O3' U R 442 " pdb=" P U R 443 " pdb=" OP1 U R 443 " ideal model delta sigma weight residual 108.00 82.20 25.80 3.00e+00 1.11e-01 7.40e+01 angle pdb=" N GLU J 528 " pdb=" CA GLU J 528 " pdb=" C GLU J 528 " ideal model delta sigma weight residual 114.75 104.43 10.32 1.26e+00 6.30e-01 6.71e+01 ... (remaining 61673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 25275 35.91 - 71.83: 1431 71.83 - 107.74: 154 107.74 - 143.66: 8 143.66 - 179.57: 14 Dihedral angle restraints: 26882 sinusoidal: 14362 harmonic: 12520 Sorted by residual: dihedral pdb=" CA ARG C 12 " pdb=" C ARG C 12 " pdb=" N PRO C 13 " pdb=" CA PRO C 13 " ideal model delta harmonic sigma weight residual 180.00 56.69 123.31 0 5.00e+00 4.00e-02 6.08e+02 dihedral pdb=" CA THR X 379 " pdb=" C THR X 379 " pdb=" N LEU X 380 " pdb=" CA LEU X 380 " ideal model delta harmonic sigma weight residual 180.00 121.71 58.29 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA LEU X 674 " pdb=" C LEU X 674 " pdb=" N ASP X 675 " pdb=" CA ASP X 675 " ideal model delta harmonic sigma weight residual 180.00 130.86 49.14 0 5.00e+00 4.00e-02 9.66e+01 ... (remaining 26879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.383: 7742 0.383 - 0.765: 6 0.765 - 1.148: 0 1.148 - 1.531: 0 1.531 - 1.914: 1 Chirality restraints: 7749 Sorted by residual: chirality pdb=" P U R 443 " pdb=" OP1 U R 443 " pdb=" OP2 U R 443 " pdb=" O5' U R 443 " both_signs ideal model delta sigma weight residual True 2.41 0.50 1.91 2.00e-01 2.50e+01 9.16e+01 chirality pdb=" CA ASP E 324 " pdb=" N ASP E 324 " pdb=" C ASP E 324 " pdb=" CB ASP E 324 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" CB VAL D 137 " pdb=" CA VAL D 137 " pdb=" CG1 VAL D 137 " pdb=" CG2 VAL D 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 7746 not shown) Planarity restraints: 5874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 12 " 1.059 9.50e-02 1.11e+02 4.74e-01 1.36e+02 pdb=" NE ARG C 12 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG C 12 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 12 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 12 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 316 " 0.039 2.00e-02 2.50e+03 3.17e-02 2.01e+01 pdb=" CG TYR D 316 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TYR D 316 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR D 316 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 316 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 316 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 316 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR D 316 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 150 " 0.033 2.00e-02 2.50e+03 2.60e-02 1.35e+01 pdb=" CG TYR D 150 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR D 150 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 150 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 150 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR D 150 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 150 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR D 150 " 0.006 2.00e-02 2.50e+03 ... (remaining 5871 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 4050 2.73 - 3.27: 38806 3.27 - 3.81: 71747 3.81 - 4.36: 82970 4.36 - 4.90: 128577 Nonbonded interactions: 326150 Sorted by model distance: nonbonded pdb=" OD1 ASN C 15 " pdb=" N LYS C 16 " model vdw 2.186 2.520 nonbonded pdb=" O2 U R 217 " pdb=" O6 G R 220 " model vdw 2.198 2.432 nonbonded pdb=" O2' U R 16 " pdb=" OP2 C R 168 " model vdw 2.234 2.440 nonbonded pdb=" OE1 GLU D 372 " pdb=" OH TYR D 391 " model vdw 2.234 2.440 nonbonded pdb=" O2' A r -2 " pdb=" OP1 G r -1 " model vdw 2.238 2.440 ... (remaining 326145 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 group one per residue 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.980 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 122.700 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.011 0.150 43320 Z= 0.679 Angle : 1.167 25.822 61678 Z= 0.647 Chirality : 0.065 1.914 7749 Planarity : 0.009 0.474 5874 Dihedral : 19.809 179.569 18702 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.93 % Favored : 92.44 % Rotamer: Outliers : 3.35 % Allowed : 7.51 % Favored : 89.14 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 1.29 % Twisted General : 0.57 % 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: -3.75 (0.11), residues: 4140 helix: -2.31 (0.08), residues: 2081 sheet: -2.63 (0.27), residues: 299 loop : -2.54 (0.13), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP E 362 HIS 0.022 0.003 HIS D 140 PHE 0.053 0.004 PHE D 77 TYR 0.077 0.004 TYR D 316 ARG 0.015 0.002 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 423 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6075 (tt) REVERT: B 87 MET cc_start: 0.7291 (mmt) cc_final: 0.7052 (mmm) REVERT: B 103 ASP cc_start: 0.7958 (t70) cc_final: 0.7487 (t70) REVERT: B 124 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7055 (mtt90) REVERT: B 135 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.6265 (ttpt) REVERT: C 12 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7407 (mtp180) REVERT: C 62 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8147 (tt) REVERT: C 71 SER cc_start: 0.8475 (m) cc_final: 0.8197 (t) REVERT: C 88 ASP cc_start: 0.6873 (m-30) cc_final: 0.6508 (p0) REVERT: D 367 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8941 (tt) REVERT: D 411 GLN cc_start: 0.7612 (mt0) cc_final: 0.7311 (mt0) REVERT: D 446 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7478 (mt0) REVERT: D 477 MET cc_start: 0.8092 (tpt) cc_final: 0.7700 (tpp) REVERT: E 315 GLN cc_start: 0.7527 (mm110) cc_final: 0.7260 (tm-30) REVERT: E 454 TYR cc_start: 0.8630 (m-80) cc_final: 0.8381 (m-80) REVERT: E 507 ASP cc_start: 0.7240 (m-30) cc_final: 0.6986 (m-30) REVERT: F 317 ILE cc_start: 0.8917 (tt) cc_final: 0.8570 (mt) REVERT: F 332 TYR cc_start: 0.9008 (m-80) cc_final: 0.8724 (m-80) REVERT: F 368 MET cc_start: 0.8535 (tpp) cc_final: 0.7802 (tpp) REVERT: F 410 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8805 (tt) REVERT: G 89 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8025 (tm) REVERT: I 10 GLU cc_start: 0.7945 (tp30) cc_final: 0.7554 (tp30) REVERT: I 78 ILE cc_start: 0.7914 (pt) cc_final: 0.7650 (tp) REVERT: I 210 ARG cc_start: 0.8141 (ttp-110) cc_final: 0.7229 (tpm170) REVERT: I 238 ARG cc_start: 0.7657 (tpp80) cc_final: 0.7392 (ttp80) REVERT: I 240 MET cc_start: 0.6449 (mmp) cc_final: 0.6073 (mmp) REVERT: K 127 LYS cc_start: 0.7756 (ttpt) cc_final: 0.6978 (tmtt) REVERT: K 128 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6492 (tt0) REVERT: L 109 ASP cc_start: 0.7942 (t0) cc_final: 0.7699 (t0) REVERT: M 18 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8501 (mm) REVERT: M 39 VAL cc_start: 0.9182 (t) cc_final: 0.8950 (m) REVERT: Q 6 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7921 (mt-10) REVERT: Q 45 GLU cc_start: 0.8253 (tt0) cc_final: 0.8017 (tt0) outliers start: 78 outliers final: 43 residues processed: 492 average time/residue: 0.5224 time to fit residues: 416.4450 Evaluate side-chains 332 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 279 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 263 TYR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 446 GLN Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 HIS Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 63 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 390 optimal weight: 7.9990 chunk 350 optimal weight: 30.0000 chunk 194 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 236 optimal weight: 50.0000 chunk 187 optimal weight: 2.9990 chunk 362 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 220 optimal weight: 5.9990 chunk 270 optimal weight: 0.5980 chunk 420 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN B 40 ASN B 47 ASN B 80 ASN C 30 ASN D 9 HIS D 72 ASN D 102 ASN D 153 GLN D 298 ASN D 393 GLN D 411 GLN D 417 ASN D 437 GLN D 443 ASN E 318 ASN E 348 ASN E 349 ASN E 352 ASN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN E 582 GLN E 617 ASN F 301 GLN ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN F 312 ASN F 334 GLN F 375 ASN F 411 GLN F 497 GLN F 515 GLN ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 GLN I 76 HIS I 118 ASN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN L 114 ASN M 51 ASN M 86 ASN N 17 HIS ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN O 24 GLN P 24 ASN P 47 ASN P 50 ASN P 65 HIS Q 66 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 43320 Z= 0.252 Angle : 0.671 26.206 61678 Z= 0.351 Chirality : 0.045 1.871 7749 Planarity : 0.005 0.081 5874 Dihedral : 20.873 179.514 13555 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.89 % Favored : 93.77 % Rotamer: Outliers : 5.37 % Allowed : 10.78 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 1.29 % Twisted General : 0.37 % 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: -1.73 (0.12), residues: 4140 helix: -0.27 (0.11), residues: 2147 sheet: -2.13 (0.27), residues: 319 loop : -2.04 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 48 HIS 0.007 0.001 HIS H 45 PHE 0.027 0.002 PHE O 32 TYR 0.033 0.002 TYR D 316 ARG 0.008 0.001 ARG I 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 326 time to evaluate : 3.368 Fit side-chains revert: symmetry clash REVERT: B 87 MET cc_start: 0.7207 (mmt) cc_final: 0.6956 (mmm) REVERT: B 103 ASP cc_start: 0.7830 (t70) cc_final: 0.7282 (t70) REVERT: C 71 SER cc_start: 0.8840 (m) cc_final: 0.8363 (t) REVERT: C 78 PHE cc_start: 0.7558 (m-80) cc_final: 0.6891 (m-80) REVERT: C 84 GLN cc_start: 0.7490 (mm110) cc_final: 0.7188 (tp-100) REVERT: C 88 ASP cc_start: 0.6518 (m-30) cc_final: 0.6252 (p0) REVERT: D 7 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7921 (tp) REVERT: D 250 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8163 (tm-30) REVERT: D 477 MET cc_start: 0.7998 (tpt) cc_final: 0.7673 (tpp) REVERT: D 518 LEU cc_start: 0.9387 (tp) cc_final: 0.9080 (mt) REVERT: E 507 ASP cc_start: 0.7197 (m-30) cc_final: 0.6873 (m-30) REVERT: E 517 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8922 (mm) REVERT: F 332 TYR cc_start: 0.8942 (m-80) cc_final: 0.8651 (m-80) REVERT: F 368 MET cc_start: 0.8623 (tpp) cc_final: 0.7935 (tpp) REVERT: G 248 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8349 (tt) REVERT: I 10 GLU cc_start: 0.8115 (tp30) cc_final: 0.7597 (tp30) REVERT: I 78 ILE cc_start: 0.7898 (pt) cc_final: 0.7633 (tp) REVERT: I 104 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7663 (t80) REVERT: I 210 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7360 (tpm170) REVERT: I 238 ARG cc_start: 0.7733 (tpp80) cc_final: 0.7458 (ttp80) REVERT: K 19 LYS cc_start: 0.8543 (tttp) cc_final: 0.8287 (ttmm) REVERT: K 107 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7355 (mt-10) REVERT: K 127 LYS cc_start: 0.7896 (ttpt) cc_final: 0.7130 (mmtt) REVERT: M 39 VAL cc_start: 0.9107 (t) cc_final: 0.8838 (m) REVERT: N 45 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8157 (ttt-90) REVERT: N 46 ASP cc_start: 0.8064 (t70) cc_final: 0.7736 (t70) REVERT: Q 45 GLU cc_start: 0.7979 (tt0) cc_final: 0.7761 (tt0) outliers start: 125 outliers final: 66 residues processed: 424 average time/residue: 0.4949 time to fit residues: 353.6501 Evaluate side-chains 335 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 264 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain H residue 3 ASP Chi-restraints excluded: chain H residue 22 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 34 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 233 optimal weight: 50.0000 chunk 130 optimal weight: 5.9990 chunk 349 optimal weight: 20.0000 chunk 286 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 421 optimal weight: 0.0670 chunk 455 optimal weight: 30.0000 chunk 375 optimal weight: 30.0000 chunk 417 optimal weight: 8.9990 chunk 143 optimal weight: 0.7980 chunk 337 optimal weight: 7.9990 overall best weight: 2.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 400 ASN E 318 ASN E 563 HIS F 306 HIS F 354 GLN F 432 ASN ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 ASN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN M 52 HIS O 22 GLN O 24 GLN P 25 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 43320 Z= 0.361 Angle : 0.683 26.350 61678 Z= 0.354 Chirality : 0.046 1.873 7749 Planarity : 0.004 0.071 5874 Dihedral : 20.658 179.938 13492 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.03 % Favored : 92.78 % Rotamer: Outliers : 5.80 % Allowed : 13.22 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 1.29 % Twisted General : 0.15 % 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: -0.92 (0.13), residues: 4140 helix: 0.56 (0.11), residues: 2153 sheet: -1.96 (0.27), residues: 323 loop : -1.87 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 186 HIS 0.007 0.001 HIS Q 55 PHE 0.028 0.002 PHE D 397 TYR 0.034 0.002 TYR D 316 ARG 0.005 0.001 ARG I 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 268 time to evaluate : 3.573 Fit side-chains revert: symmetry clash REVERT: B 103 ASP cc_start: 0.7905 (t70) cc_final: 0.7356 (t70) REVERT: B 138 GLN cc_start: 0.8056 (pm20) cc_final: 0.7579 (pm20) REVERT: C 71 SER cc_start: 0.8692 (m) cc_final: 0.8288 (t) REVERT: C 78 PHE cc_start: 0.7436 (m-80) cc_final: 0.6671 (m-10) REVERT: C 88 ASP cc_start: 0.7173 (m-30) cc_final: 0.6718 (p0) REVERT: D 7 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8081 (tp) REVERT: D 303 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8878 (mp) REVERT: E 507 ASP cc_start: 0.7281 (m-30) cc_final: 0.7046 (m-30) REVERT: E 517 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8971 (mm) REVERT: F 314 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8915 (p) REVERT: F 332 TYR cc_start: 0.8916 (m-80) cc_final: 0.8716 (m-80) REVERT: F 368 MET cc_start: 0.8668 (tpp) cc_final: 0.7545 (tpp) REVERT: G 122 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8844 (tt) REVERT: G 248 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8413 (tt) REVERT: G 260 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8537 (pp) REVERT: I 10 GLU cc_start: 0.8145 (tp30) cc_final: 0.7660 (tp30) REVERT: I 78 ILE cc_start: 0.7883 (pt) cc_final: 0.7674 (tp) REVERT: I 104 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7569 (t80) REVERT: I 210 ARG cc_start: 0.7957 (ttp-110) cc_final: 0.7095 (tpm170) REVERT: I 238 ARG cc_start: 0.7786 (tpp80) cc_final: 0.7469 (ttp80) REVERT: K 82 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8437 (mt) REVERT: K 107 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7529 (mt-10) REVERT: M 39 VAL cc_start: 0.9142 (t) cc_final: 0.8786 (m) REVERT: Q 45 GLU cc_start: 0.8194 (tt0) cc_final: 0.7903 (tt0) outliers start: 135 outliers final: 93 residues processed: 372 average time/residue: 0.4827 time to fit residues: 309.2569 Evaluate side-chains 353 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 251 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 448 TYR Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain H residue 3 ASP Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 416 optimal weight: 20.0000 chunk 316 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 282 optimal weight: 0.2980 chunk 422 optimal weight: 40.0000 chunk 447 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 chunk 400 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 563 HIS F 334 GLN G 90 HIS ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 43320 Z= 0.422 Angle : 0.699 26.304 61678 Z= 0.360 Chirality : 0.047 1.873 7749 Planarity : 0.005 0.076 5874 Dihedral : 20.624 179.633 13483 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.10 % Favored : 92.75 % Rotamer: Outliers : 6.91 % Allowed : 14.17 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 1.29 % Twisted General : 0.12 % 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: -0.72 (0.13), residues: 4140 helix: 0.80 (0.11), residues: 2154 sheet: -1.85 (0.28), residues: 323 loop : -1.90 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 186 HIS 0.009 0.002 HIS Q 55 PHE 0.028 0.002 PHE G 64 TYR 0.031 0.002 TYR D 316 ARG 0.007 0.001 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 262 time to evaluate : 3.429 Fit side-chains revert: symmetry clash REVERT: B 87 MET cc_start: 0.7299 (mmt) cc_final: 0.7028 (mmm) REVERT: B 103 ASP cc_start: 0.7768 (t70) cc_final: 0.7265 (t70) REVERT: B 138 GLN cc_start: 0.8061 (pm20) cc_final: 0.7744 (pm20) REVERT: C 71 SER cc_start: 0.8622 (m) cc_final: 0.8295 (t) REVERT: C 73 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6181 (ptm) REVERT: C 78 PHE cc_start: 0.7613 (m-80) cc_final: 0.6823 (m-10) REVERT: C 107 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7598 (mtm180) REVERT: F 314 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8958 (p) REVERT: F 341 TYR cc_start: 0.9067 (OUTLIER) cc_final: 0.8809 (p90) REVERT: F 368 MET cc_start: 0.8710 (tpp) cc_final: 0.7615 (tpp) REVERT: F 410 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8942 (tt) REVERT: G 122 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9070 (tt) REVERT: G 260 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8587 (pp) REVERT: I 10 GLU cc_start: 0.8164 (tp30) cc_final: 0.7725 (tp30) REVERT: I 104 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7498 (t80) REVERT: I 210 ARG cc_start: 0.7989 (ttp-110) cc_final: 0.7106 (tpm170) REVERT: I 227 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8459 (mm) REVERT: I 238 ARG cc_start: 0.7848 (tpp80) cc_final: 0.7459 (ttp80) REVERT: K 19 LYS cc_start: 0.8649 (tttp) cc_final: 0.8424 (ttmt) REVERT: K 64 ARG cc_start: 0.6604 (mmp80) cc_final: 0.6252 (ttt90) REVERT: K 82 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8404 (mt) REVERT: K 107 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7433 (mt-10) REVERT: L 74 THR cc_start: 0.7271 (OUTLIER) cc_final: 0.6983 (p) REVERT: P 82 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8229 (ptm-80) REVERT: Q 45 GLU cc_start: 0.8353 (tt0) cc_final: 0.8006 (tt0) outliers start: 161 outliers final: 112 residues processed: 391 average time/residue: 0.4716 time to fit residues: 313.9343 Evaluate side-chains 369 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 245 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 448 TYR Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain F residue 432 ASN Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain H residue 3 ASP Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 22 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 372 optimal weight: 40.0000 chunk 254 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 333 optimal weight: 20.0000 chunk 184 optimal weight: 0.9990 chunk 381 optimal weight: 50.0000 chunk 309 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 401 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 HIS G 207 HIS ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 43320 Z= 0.357 Angle : 0.653 26.297 61678 Z= 0.336 Chirality : 0.046 1.872 7749 Planarity : 0.004 0.072 5874 Dihedral : 20.529 179.138 13479 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.79 % Favored : 93.09 % Rotamer: Outliers : 7.39 % Allowed : 14.64 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 0.65 % Twisted General : 0.10 % 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 (0.13), residues: 4140 helix: 1.10 (0.12), residues: 2155 sheet: -1.80 (0.28), residues: 323 loop : -1.83 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 186 HIS 0.008 0.001 HIS Q 55 PHE 0.021 0.002 PHE O 32 TYR 0.032 0.002 TYR B 8 ARG 0.007 0.001 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 262 time to evaluate : 5.404 Fit side-chains revert: symmetry clash REVERT: A 83 GLN cc_start: 0.6052 (OUTLIER) cc_final: 0.5794 (mp10) REVERT: B 87 MET cc_start: 0.7292 (mmt) cc_final: 0.7012 (mmm) REVERT: B 103 ASP cc_start: 0.7785 (t70) cc_final: 0.7205 (t70) REVERT: B 138 GLN cc_start: 0.8174 (pm20) cc_final: 0.7880 (pm20) REVERT: C 71 SER cc_start: 0.8639 (m) cc_final: 0.8289 (t) REVERT: C 73 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6094 (ptm) REVERT: C 78 PHE cc_start: 0.7578 (m-80) cc_final: 0.6791 (m-10) REVERT: C 88 ASP cc_start: 0.7081 (m-30) cc_final: 0.6700 (p0) REVERT: C 107 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7614 (mtm180) REVERT: D 44 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8007 (tt) REVERT: D 303 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8861 (mp) REVERT: D 495 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9034 (mm) REVERT: E 517 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8933 (mm) REVERT: F 314 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8966 (p) REVERT: F 332 TYR cc_start: 0.8986 (m-80) cc_final: 0.8699 (m-80) REVERT: F 341 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8841 (p90) REVERT: F 410 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8987 (tt) REVERT: G 122 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9100 (tt) REVERT: G 204 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7289 (ptpp) REVERT: G 248 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8342 (tt) REVERT: G 260 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8644 (pp) REVERT: I 10 GLU cc_start: 0.8073 (tp30) cc_final: 0.7659 (tp30) REVERT: I 104 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7363 (t80) REVERT: I 210 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7101 (tpm170) REVERT: I 238 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7558 (ttp80) REVERT: K 19 LYS cc_start: 0.8632 (tttp) cc_final: 0.8407 (ttmt) REVERT: K 64 ARG cc_start: 0.6501 (mmp80) cc_final: 0.6190 (ttt90) REVERT: K 107 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7417 (mt-10) REVERT: K 109 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8377 (mm) REVERT: L 74 THR cc_start: 0.7236 (OUTLIER) cc_final: 0.6968 (p) REVERT: M 39 VAL cc_start: 0.9155 (t) cc_final: 0.8862 (m) REVERT: N 33 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8923 (tp) REVERT: N 35 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7421 (mm-30) REVERT: P 82 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8328 (ptm-80) REVERT: Q 45 GLU cc_start: 0.8324 (tt0) cc_final: 0.7978 (tt0) outliers start: 172 outliers final: 118 residues processed: 402 average time/residue: 0.4656 time to fit residues: 321.5978 Evaluate side-chains 382 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 245 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 448 TYR Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 518 THR Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain F residue 432 ASN Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain H residue 3 ASP Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 22 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 150 optimal weight: 0.8980 chunk 403 optimal weight: 50.0000 chunk 88 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 447 optimal weight: 30.0000 chunk 371 optimal weight: 40.0000 chunk 207 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 235 optimal weight: 20.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 83 GLN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 HIS G 207 HIS H 10 GLN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN P 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43320 Z= 0.196 Angle : 0.564 26.271 61678 Z= 0.289 Chirality : 0.043 1.871 7749 Planarity : 0.004 0.068 5874 Dihedral : 20.335 178.855 13476 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.46 % Favored : 94.42 % Rotamer: Outliers : 5.75 % Allowed : 16.75 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 0.65 % Twisted General : 0.10 % 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: 0.06 (0.14), residues: 4140 helix: 1.51 (0.12), residues: 2165 sheet: -1.61 (0.28), residues: 337 loop : -1.64 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 186 HIS 0.005 0.001 HIS D 140 PHE 0.019 0.001 PHE O 32 TYR 0.019 0.001 TYR B 8 ARG 0.004 0.000 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 282 time to evaluate : 3.812 Fit side-chains REVERT: A 74 ILE cc_start: 0.7952 (tt) cc_final: 0.7646 (mm) REVERT: B 22 LYS cc_start: 0.8290 (tptp) cc_final: 0.8062 (tptp) REVERT: B 87 MET cc_start: 0.7050 (mmt) cc_final: 0.6820 (mmm) REVERT: B 103 ASP cc_start: 0.7695 (t70) cc_final: 0.7119 (t70) REVERT: B 105 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9189 (mt) REVERT: B 138 GLN cc_start: 0.8116 (pm20) cc_final: 0.7839 (pm20) REVERT: C 7 GLN cc_start: 0.8273 (tt0) cc_final: 0.7821 (tt0) REVERT: C 71 SER cc_start: 0.8636 (m) cc_final: 0.8237 (t) REVERT: C 73 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5558 (ptm) REVERT: C 78 PHE cc_start: 0.7589 (m-80) cc_final: 0.6903 (m-80) REVERT: C 107 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7397 (mtm180) REVERT: D 495 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8885 (mm) REVERT: E 447 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.7086 (p0) REVERT: E 517 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8969 (mm) REVERT: E 587 ILE cc_start: 0.8963 (pt) cc_final: 0.8757 (pt) REVERT: F 368 MET cc_start: 0.8649 (tpp) cc_final: 0.7568 (tpp) REVERT: G 122 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9043 (tt) REVERT: G 204 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6752 (ptpp) REVERT: G 260 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8485 (pp) REVERT: I 10 GLU cc_start: 0.8019 (tp30) cc_final: 0.7581 (tp30) REVERT: I 104 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7474 (t80) REVERT: I 120 LYS cc_start: 0.5547 (mtpp) cc_final: 0.5167 (pttp) REVERT: I 210 ARG cc_start: 0.8097 (ttp-110) cc_final: 0.7129 (tpp-160) REVERT: I 238 ARG cc_start: 0.7668 (tpp80) cc_final: 0.7399 (ttp80) REVERT: K 64 ARG cc_start: 0.6493 (mmp80) cc_final: 0.5948 (ttt90) REVERT: K 82 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8452 (mt) REVERT: K 107 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7539 (mt-10) REVERT: L 74 THR cc_start: 0.7527 (OUTLIER) cc_final: 0.7186 (p) REVERT: M 39 VAL cc_start: 0.9034 (t) cc_final: 0.8705 (m) REVERT: N 35 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7421 (mm-30) REVERT: P 82 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8245 (ptm-80) outliers start: 134 outliers final: 88 residues processed: 391 average time/residue: 0.4815 time to fit residues: 321.8060 Evaluate side-chains 361 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 260 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 447 ASN Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 518 THR Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 432 ASN Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 17 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 431 optimal weight: 0.0020 chunk 50 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 327 optimal weight: 10.0000 chunk 253 optimal weight: 0.0050 chunk 377 optimal weight: 0.0670 chunk 250 optimal weight: 1.9990 chunk 446 optimal weight: 8.9990 chunk 279 optimal weight: 4.9990 chunk 272 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 HIS C 26 HIS C 28 ASN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 HIS ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 GLN ** Q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 43320 Z= 0.148 Angle : 0.540 26.273 61678 Z= 0.275 Chirality : 0.042 1.872 7749 Planarity : 0.003 0.065 5874 Dihedral : 20.198 179.266 13470 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.29 % Favored : 94.59 % Rotamer: Outliers : 4.51 % Allowed : 18.81 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 0.65 % Twisted General : 0.10 % 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: 0.38 (0.14), residues: 4140 helix: 1.79 (0.12), residues: 2161 sheet: -1.44 (0.28), residues: 322 loop : -1.52 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 186 HIS 0.014 0.001 HIS G 207 PHE 0.016 0.001 PHE O 32 TYR 0.016 0.001 TYR B 8 ARG 0.005 0.000 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 287 time to evaluate : 3.669 Fit side-chains REVERT: A 74 ILE cc_start: 0.7969 (tt) cc_final: 0.7626 (mm) REVERT: A 89 LEU cc_start: 0.1946 (tp) cc_final: 0.1529 (mt) REVERT: B 103 ASP cc_start: 0.7560 (t70) cc_final: 0.6953 (t70) REVERT: B 105 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9146 (mt) REVERT: C 7 GLN cc_start: 0.8102 (tt0) cc_final: 0.7623 (tt0) REVERT: C 71 SER cc_start: 0.8629 (m) cc_final: 0.8205 (t) REVERT: C 73 MET cc_start: 0.6140 (OUTLIER) cc_final: 0.5576 (ptm) REVERT: C 78 PHE cc_start: 0.7658 (m-80) cc_final: 0.7147 (m-80) REVERT: C 88 ASP cc_start: 0.7058 (m-30) cc_final: 0.6444 (p0) REVERT: C 107 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7383 (mtm180) REVERT: C 108 MET cc_start: 0.8751 (pmt) cc_final: 0.8548 (pmm) REVERT: D 303 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8596 (mp) REVERT: D 495 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8805 (mm) REVERT: E 447 ASN cc_start: 0.7082 (OUTLIER) cc_final: 0.6835 (p0) REVERT: E 517 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8920 (mm) REVERT: F 368 MET cc_start: 0.8639 (tpp) cc_final: 0.7852 (tpp) REVERT: G 122 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9030 (tt) REVERT: G 260 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8488 (pp) REVERT: I 10 GLU cc_start: 0.8021 (tp30) cc_final: 0.7533 (tp30) REVERT: I 104 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7482 (t80) REVERT: I 120 LYS cc_start: 0.5579 (mtpp) cc_final: 0.5228 (pttp) REVERT: I 210 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7163 (tpm170) REVERT: I 238 ARG cc_start: 0.7651 (tpp80) cc_final: 0.7315 (ttp80) REVERT: I 241 LYS cc_start: 0.6616 (tptp) cc_final: 0.5682 (pttt) REVERT: K 64 ARG cc_start: 0.6551 (mmp80) cc_final: 0.5930 (ttt90) REVERT: K 82 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8486 (mt) REVERT: K 107 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7453 (mt-10) REVERT: L 74 THR cc_start: 0.6976 (OUTLIER) cc_final: 0.6769 (p) REVERT: M 39 VAL cc_start: 0.8774 (t) cc_final: 0.8506 (m) REVERT: N 92 MET cc_start: 0.8106 (tpp) cc_final: 0.7876 (tpp) REVERT: P 82 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8112 (ptm-80) REVERT: Q 36 LEU cc_start: 0.8621 (tp) cc_final: 0.8375 (tp) outliers start: 105 outliers final: 71 residues processed: 374 average time/residue: 0.4835 time to fit residues: 305.7641 Evaluate side-chains 350 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 266 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 447 ASN Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 518 THR Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 432 ASN Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 39 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 276 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 266 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 283 optimal weight: 1.9990 chunk 304 optimal weight: 0.0970 chunk 220 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 350 optimal weight: 30.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 GLN E 563 HIS F 354 GLN F 407 GLN I 106 ASN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 43320 Z= 0.152 Angle : 0.536 26.261 61678 Z= 0.272 Chirality : 0.041 1.872 7749 Planarity : 0.003 0.064 5874 Dihedral : 20.080 179.894 13467 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.07 % Favored : 94.81 % Rotamer: Outliers : 4.59 % Allowed : 18.68 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 0.65 % Twisted General : 0.10 % 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: 0.66 (0.14), residues: 4140 helix: 2.04 (0.12), residues: 2141 sheet: -1.30 (0.29), residues: 306 loop : -1.40 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 186 HIS 0.005 0.001 HIS A 67 PHE 0.015 0.001 PHE O 32 TYR 0.016 0.001 TYR B 8 ARG 0.006 0.000 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 283 time to evaluate : 3.864 Fit side-chains REVERT: A 74 ILE cc_start: 0.7892 (tt) cc_final: 0.7649 (mm) REVERT: A 89 LEU cc_start: 0.1921 (tp) cc_final: 0.1483 (mt) REVERT: B 103 ASP cc_start: 0.7565 (t70) cc_final: 0.6947 (t70) REVERT: B 105 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9115 (mt) REVERT: C 7 GLN cc_start: 0.7978 (tt0) cc_final: 0.7212 (tt0) REVERT: C 71 SER cc_start: 0.8650 (m) cc_final: 0.8201 (t) REVERT: C 73 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.5435 (ptm) REVERT: C 78 PHE cc_start: 0.7677 (m-80) cc_final: 0.7174 (m-80) REVERT: C 88 ASP cc_start: 0.6978 (m-30) cc_final: 0.6286 (p0) REVERT: C 107 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7352 (mtm180) REVERT: C 108 MET cc_start: 0.8651 (pmt) cc_final: 0.8398 (pmm) REVERT: D 303 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8574 (mp) REVERT: D 495 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8760 (mm) REVERT: E 447 ASN cc_start: 0.7124 (OUTLIER) cc_final: 0.6872 (p0) REVERT: E 517 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8965 (mm) REVERT: E 613 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: F 368 MET cc_start: 0.8670 (tpp) cc_final: 0.7839 (tpp) REVERT: G 122 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9036 (tt) REVERT: G 260 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8333 (pp) REVERT: I 10 GLU cc_start: 0.8088 (tp30) cc_final: 0.7569 (tp30) REVERT: I 104 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7528 (t80) REVERT: I 116 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.5881 (tp) REVERT: I 120 LYS cc_start: 0.5530 (mtpp) cc_final: 0.5170 (pttp) REVERT: I 210 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7038 (tpm170) REVERT: I 238 ARG cc_start: 0.7602 (tpp80) cc_final: 0.7270 (ttp80) REVERT: I 241 LYS cc_start: 0.6678 (tptp) cc_final: 0.5827 (pttt) REVERT: K 64 ARG cc_start: 0.6546 (mmp80) cc_final: 0.5907 (ttt90) REVERT: K 82 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8479 (mt) REVERT: K 107 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7476 (mt-10) REVERT: L 1 MET cc_start: 0.6993 (OUTLIER) cc_final: 0.6239 (ttm) REVERT: L 109 ASP cc_start: 0.7326 (t0) cc_final: 0.7020 (m-30) REVERT: M 39 VAL cc_start: 0.8683 (t) cc_final: 0.8426 (m) REVERT: N 92 MET cc_start: 0.8098 (tpp) cc_final: 0.7868 (tpp) REVERT: P 47 ASN cc_start: 0.7614 (t0) cc_final: 0.7181 (t0) REVERT: P 82 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8291 (ptm-80) REVERT: Q 36 LEU cc_start: 0.8549 (tp) cc_final: 0.8341 (tp) outliers start: 107 outliers final: 72 residues processed: 367 average time/residue: 0.4855 time to fit residues: 306.4299 Evaluate side-chains 356 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 269 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 447 ASN Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 518 THR Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 613 GLN Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 432 ASN Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 39 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 405 optimal weight: 6.9990 chunk 427 optimal weight: 50.0000 chunk 390 optimal weight: 40.0000 chunk 415 optimal weight: 50.0000 chunk 250 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 326 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 375 optimal weight: 20.0000 chunk 393 optimal weight: 40.0000 chunk 414 optimal weight: 30.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 36 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN E 563 HIS ** F 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 GLN P 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.132 43320 Z= 0.681 Angle : 0.827 26.126 61678 Z= 0.422 Chirality : 0.052 1.884 7749 Planarity : 0.005 0.077 5874 Dihedral : 20.413 178.348 13465 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.78 % Favored : 92.10 % Rotamer: Outliers : 5.07 % Allowed : 19.19 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 0.65 % Twisted General : 0.10 % 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: -0.26 (0.13), residues: 4140 helix: 1.23 (0.11), residues: 2162 sheet: -1.58 (0.30), residues: 302 loop : -1.81 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 186 HIS 0.011 0.003 HIS Q 55 PHE 0.034 0.003 PHE E 477 TYR 0.034 0.003 TYR B 8 ARG 0.014 0.001 ARG K 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 237 time to evaluate : 3.619 Fit side-chains REVERT: B 103 ASP cc_start: 0.7942 (t70) cc_final: 0.7253 (t70) REVERT: B 194 TYR cc_start: 0.8550 (t80) cc_final: 0.8313 (t80) REVERT: C 71 SER cc_start: 0.8782 (m) cc_final: 0.8445 (t) REVERT: C 73 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.6067 (ptm) REVERT: C 88 ASP cc_start: 0.7365 (m-30) cc_final: 0.7000 (p0) REVERT: D 44 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8201 (tt) REVERT: D 303 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8919 (mp) REVERT: D 495 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9023 (mm) REVERT: E 310 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8227 (t) REVERT: E 613 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: F 368 MET cc_start: 0.8684 (tpp) cc_final: 0.7884 (tpp) REVERT: G 122 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9012 (tt) REVERT: G 260 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8793 (pp) REVERT: I 10 GLU cc_start: 0.8226 (tp30) cc_final: 0.7571 (tp30) REVERT: I 104 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7578 (t80) REVERT: I 210 ARG cc_start: 0.8132 (ttp-110) cc_final: 0.7171 (tpm170) REVERT: I 238 ARG cc_start: 0.7718 (tpp80) cc_final: 0.7332 (ttp80) REVERT: K 82 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8460 (mt) REVERT: K 107 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7470 (mt-10) REVERT: M 39 VAL cc_start: 0.9058 (t) cc_final: 0.8751 (m) outliers start: 118 outliers final: 92 residues processed: 334 average time/residue: 0.4613 time to fit residues: 264.7620 Evaluate side-chains 330 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 228 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 518 THR Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 613 GLN Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 432 ASN Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain H residue 3 ASP Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 41 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 273 optimal weight: 0.9990 chunk 439 optimal weight: 20.0000 chunk 268 optimal weight: 0.5980 chunk 208 optimal weight: 0.5980 chunk 305 optimal weight: 0.6980 chunk 461 optimal weight: 6.9990 chunk 424 optimal weight: 0.9990 chunk 367 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 283 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 HIS F 334 GLN F 518 ASN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN P 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43320 Z= 0.186 Angle : 0.577 26.219 61678 Z= 0.294 Chirality : 0.043 1.872 7749 Planarity : 0.004 0.066 5874 Dihedral : 20.218 178.451 13465 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.36 % Favored : 94.52 % Rotamer: Outliers : 3.69 % Allowed : 20.78 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 0.65 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 4140 helix: 1.76 (0.12), residues: 2146 sheet: -1.40 (0.30), residues: 311 loop : -1.51 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 186 HIS 0.005 0.001 HIS E 563 PHE 0.020 0.001 PHE O 32 TYR 0.020 0.002 TYR G 243 ARG 0.009 0.000 ARG L 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 269 time to evaluate : 3.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 ASP cc_start: 0.7695 (t70) cc_final: 0.7097 (t70) REVERT: B 105 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9158 (mt) REVERT: B 138 GLN cc_start: 0.8241 (pm20) cc_final: 0.8012 (pm20) REVERT: C 71 SER cc_start: 0.8658 (m) cc_final: 0.8235 (t) REVERT: C 73 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.5576 (ptm) REVERT: C 78 PHE cc_start: 0.7778 (m-80) cc_final: 0.7187 (m-80) REVERT: C 85 GLU cc_start: 0.7400 (pp20) cc_final: 0.6981 (pp20) REVERT: C 88 ASP cc_start: 0.7044 (m-30) cc_final: 0.6437 (p0) REVERT: D 303 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8654 (mp) REVERT: D 495 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8847 (mm) REVERT: E 613 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: F 332 TYR cc_start: 0.8821 (m-80) cc_final: 0.8459 (m-80) REVERT: G 122 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9031 (tt) REVERT: G 260 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8543 (pp) REVERT: I 10 GLU cc_start: 0.7974 (tp30) cc_final: 0.7502 (tp30) REVERT: I 104 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7428 (t80) REVERT: I 210 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7130 (tpm170) REVERT: I 238 ARG cc_start: 0.7624 (tpp80) cc_final: 0.7294 (ttp80) REVERT: K 82 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8475 (mt) REVERT: K 107 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7430 (mt-10) REVERT: M 39 VAL cc_start: 0.8783 (t) cc_final: 0.8527 (m) REVERT: P 47 ASN cc_start: 0.7644 (t0) cc_final: 0.7211 (t0) REVERT: P 82 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8234 (ptm-80) REVERT: Q 11 MET cc_start: 0.8471 (mmm) cc_final: 0.8222 (mmm) outliers start: 86 outliers final: 69 residues processed: 341 average time/residue: 0.4743 time to fit residues: 275.9168 Evaluate side-chains 335 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 256 time to evaluate : 3.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 518 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 613 GLN Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 291 optimal weight: 0.7980 chunk 391 optimal weight: 50.0000 chunk 112 optimal weight: 6.9990 chunk 338 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 367 optimal weight: 8.9990 chunk 153 optimal weight: 0.0570 chunk 377 optimal weight: 50.0000 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 HIS F 334 GLN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.178286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.131821 restraints weight = 79635.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121440 restraints weight = 110381.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.117723 restraints weight = 99063.354| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 43320 Z= 0.232 Angle : 0.581 26.198 61678 Z= 0.296 Chirality : 0.043 1.876 7749 Planarity : 0.004 0.070 5874 Dihedral : 20.164 179.994 13465 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 3.91 % Allowed : 20.82 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 0.65 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 4140 helix: 1.91 (0.12), residues: 2140 sheet: -1.41 (0.30), residues: 312 loop : -1.45 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 147 HIS 0.006 0.001 HIS A 67 PHE 0.022 0.001 PHE O 32 TYR 0.023 0.002 TYR B 8 ARG 0.004 0.000 ARG L 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7376.53 seconds wall clock time: 134 minutes 25.41 seconds (8065.41 seconds total)