Starting phenix.real_space_refine on Tue Feb 20 03:35:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crp_30455/02_2024/7crp_30455_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crp_30455/02_2024/7crp_30455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crp_30455/02_2024/7crp_30455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crp_30455/02_2024/7crp_30455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crp_30455/02_2024/7crp_30455_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crp_30455/02_2024/7crp_30455_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12071 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 336 5.49 5 S 29 5.16 5 C 8245 2.51 5 N 2788 2.21 5 O 3432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "I ARG 1097": "NH1" <-> "NH2" Residue "I GLU 1111": "OE1" <-> "OE2" Residue "I ARG 1133": "NH1" <-> "NH2" Residue "I ARG 1142": "NH1" <-> "NH2" Residue "I ARG 1160": "NH1" <-> "NH2" Residue "I GLU 1169": "OE1" <-> "OE2" Residue "I GLU 1182": "OE1" <-> "OE2" Residue "I GLU 1193": "OE1" <-> "OE2" Residue "I ARG 1220": "NH1" <-> "NH2" Residue "I ARG 1242": "NH1" <-> "NH2" Residue "I ARG 1270": "NH1" <-> "NH2" Residue "I GLU 1272": "OE1" <-> "OE2" Residue "I ARG 1287": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14833 Number of models: 1 Model: "" Number of chains: 11 Chain: "M" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 833 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1, 'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 803 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1, 'NLE:plan-1': 2} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "A" Number of atoms: 3420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3420 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "K" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3468 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "I" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1785 Unusual residues: {' ZN': 3} Classifications: {'peptide': 223, 'undetermined': 3} Link IDs: {'PTRANS': 12, 'TRANS': 210, None: 3} Not linked: pdbres="SAM I1501 " pdbres=" ZN I1502 " Not linked: pdbres=" ZN I1502 " pdbres=" ZN I1503 " Not linked: pdbres=" ZN I1503 " pdbres=" ZN I1504 " Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14347 SG CYS I1226 39.089 63.619 56.304 1.00 79.83 S ATOM 14705 SG CYS I1273 35.850 64.429 53.660 1.00 94.82 S ATOM 14721 SG CYS I1275 38.268 64.272 51.140 1.00 82.68 S ATOM 13309 SG CYS I1098 60.107 91.817 70.409 1.00 57.92 S ATOM 13382 SG CYS I1108 59.101 92.880 65.735 1.00 57.74 S ATOM 13424 SG CYS I1114 58.558 89.544 67.760 1.00 50.22 S ATOM 13382 SG CYS I1108 59.101 92.880 65.735 1.00 57.74 S ATOM 13542 SG CYS I1128 58.192 96.211 67.575 1.00 60.95 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N SAM I1501 " occ=0.93 ... (25 atoms not shown) pdb=" O4' SAM I1501 " occ=0.93 Time building chain proxies: 8.17, per 1000 atoms: 0.55 Number of scatterers: 14833 At special positions: 0 Unit cell: (136.08, 150.12, 172.8, 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 29 16.00 P 336 15.00 O 3432 8.00 N 2788 7.00 C 8245 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: 6.86 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I1502 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1273 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1275 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1226 " pdb=" ZN I1503 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1098 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1114 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1108 " pdb=" ZN I1504 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1128 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1108 " 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 2 sheets defined 44.0% alpha, 2.2% beta 120 base pairs and 292 stacking pairs defined. Time for finding SS restraints: 8.18 Creating SS restraints... Processing helix chain 'M' and resid 48 through 54 removed outlier: 3.766A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 77 removed outlier: 3.696A pdb=" N LEU M 70 " --> pdb=" O PRO M 66 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL M 71 " --> pdb=" O PHE M 67 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG M 72 " --> pdb=" O GLN M 68 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 113 removed outlier: 3.687A pdb=" N ALA M 91 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU M 92 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN M 93 " --> pdb=" O NLE M 90 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU M 94 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER M 96 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU M 97 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL M 101 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE M 104 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU M 105 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR M 107 " --> pdb=" O PHE M 104 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN M 108 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 131 removed outlier: 3.832A pdb=" N LEU M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 28 removed outlier: 3.527A pdb=" N GLY B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 25 through 28' Processing helix chain 'B' and resid 32 through 39 removed outlier: 3.608A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.668A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.669A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 35 removed outlier: 3.569A pdb=" N HIS C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.954A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.711A pdb=" N ALA C 66 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 87 removed outlier: 3.603A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 96 No H-bonds generated for 'chain 'C' and resid 93 through 96' Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.594A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 80 removed outlier: 3.744A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 96 removed outlier: 3.721A pdb=" N THR D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 119 removed outlier: 3.838A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 51 Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.781A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 113 removed outlier: 3.651A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 131 removed outlier: 3.616A pdb=" N ALA E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 51 through 75 removed outlier: 3.984A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 93 removed outlier: 4.045A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 removed outlier: 3.530A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 17 through 21' Processing helix chain 'G' and resid 27 through 35 removed outlier: 3.740A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 55 removed outlier: 3.961A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 73 removed outlier: 3.647A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 87 removed outlier: 3.611A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'H' and resid 38 through 45 removed outlier: 4.295A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 80 removed outlier: 3.745A pdb=" N MET H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA H 74 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 98 removed outlier: 3.909A pdb=" N ARG H 96 " --> pdb=" O GLN H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 105 No H-bonds generated for 'chain 'H' and resid 103 through 105' Processing helix chain 'H' and resid 107 through 119 removed outlier: 3.614A pdb=" N VAL H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 1115 through 1118 No H-bonds generated for 'chain 'I' and resid 1115 through 1118' Processing helix chain 'I' and resid 1181 through 1192 Processing helix chain 'I' and resid 1218 through 1220 No H-bonds generated for 'chain 'I' and resid 1218 through 1220' Processing sheet with id= A, first strand: chain 'I' and resid 1177 through 1179 removed outlier: 4.177A pdb=" N ARG I1208 " --> pdb=" O THR I1205 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR I1205 " --> pdb=" O ARG I1208 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE I1210 " --> pdb=" O THR I1203 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N THR I1203 " --> pdb=" O ILE I1210 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 1230 through 1237 188 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 313 hydrogen bonds 626 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 292 stacking parallelities Total time for adding SS restraints: 5.88 Time building geometry restraints manager: 7.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2802 1.33 - 1.45: 5045 1.45 - 1.57: 7227 1.57 - 1.69: 670 1.69 - 1.81: 41 Bond restraints: 15785 Sorted by residual: bond pdb=" N ARG D 30 " pdb=" CA ARG D 30 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.74e+00 bond pdb=" CA LYS I1077 " pdb=" C LYS I1077 " ideal model delta sigma weight residual 1.519 1.557 -0.037 1.32e-02 5.74e+03 8.06e+00 bond pdb=" C2 SAM I1501 " pdb=" N3 SAM I1501 " ideal model delta sigma weight residual 1.322 1.376 -0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" C8 SAM I1501 " pdb=" N7 SAM I1501 " ideal model delta sigma weight residual 1.298 1.350 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C2 SAM I1501 " pdb=" N1 SAM I1501 " ideal model delta sigma weight residual 1.329 1.380 -0.051 2.00e-02 2.50e+03 6.62e+00 ... (remaining 15780 not shown) Histogram of bond angle deviations from ideal: 97.19 - 104.54: 1352 104.54 - 111.89: 8394 111.89 - 119.24: 4909 119.24 - 126.59: 7099 126.59 - 133.94: 1007 Bond angle restraints: 22761 Sorted by residual: angle pdb=" N LYS I1181 " pdb=" CA LYS I1181 " pdb=" C LYS I1181 " ideal model delta sigma weight residual 111.11 118.33 -7.22 1.20e+00 6.94e-01 3.62e+01 angle pdb=" N VAL M 117 " pdb=" CA VAL M 117 " pdb=" C VAL M 117 " ideal model delta sigma weight residual 113.71 108.43 5.28 9.50e-01 1.11e+00 3.09e+01 angle pdb=" C THR D 29 " pdb=" N ARG D 30 " pdb=" CA ARG D 30 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 angle pdb=" N ARG C 35 " pdb=" CA ARG C 35 " pdb=" C ARG C 35 " ideal model delta sigma weight residual 111.82 116.82 -5.00 1.16e+00 7.43e-01 1.86e+01 angle pdb=" N ARG D 30 " pdb=" CA ARG D 30 " pdb=" CB ARG D 30 " ideal model delta sigma weight residual 110.49 117.33 -6.84 1.69e+00 3.50e-01 1.64e+01 ... (remaining 22756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 6935 33.94 - 67.87: 1679 67.87 - 101.81: 19 101.81 - 135.75: 1 135.75 - 169.68: 1 Dihedral angle restraints: 8635 sinusoidal: 5739 harmonic: 2896 Sorted by residual: dihedral pdb=" CA HIS E 39 " pdb=" C HIS E 39 " pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASP I1146 " pdb=" C ASP I1146 " pdb=" N ALA I1147 " pdb=" CA ALA I1147 " ideal model delta harmonic sigma weight residual -180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA PRO I1145 " pdb=" C PRO I1145 " pdb=" N ASP I1146 " pdb=" CA ASP I1146 " ideal model delta harmonic sigma weight residual 180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 8632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1866 0.045 - 0.090: 607 0.090 - 0.134: 79 0.134 - 0.179: 18 0.179 - 0.224: 2 Chirality restraints: 2572 Sorted by residual: chirality pdb=" CA LYS I1181 " pdb=" N LYS I1181 " pdb=" C LYS I1181 " pdb=" CB LYS I1181 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ARG C 35 " pdb=" N ARG C 35 " pdb=" C ARG C 35 " pdb=" CB ARG C 35 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA SER C 113 " pdb=" N SER C 113 " pdb=" C SER C 113 " pdb=" CB SER C 113 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.98e-01 ... (remaining 2569 not shown) Planarity restraints: 1729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR I1144 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO I1145 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO I1145 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO I1145 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE I1076 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.90e+00 pdb=" C ILE I1076 " 0.034 2.00e-02 2.50e+03 pdb=" O ILE I1076 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS I1077 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C NLE E 120 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO E 121 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " 0.025 5.00e-02 4.00e+02 ... (remaining 1726 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 1 2.16 - 2.85: 4175 2.85 - 3.53: 16665 3.53 - 4.22: 37221 4.22 - 4.90: 57157 Nonbonded interactions: 115219 Sorted by model distance: nonbonded pdb=" NZ LYS G 119 " pdb=" OE2 GLU I1111 " model vdw 1.478 2.520 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.193 2.440 nonbonded pdb=" NZ LYS G 119 " pdb=" CD GLU I1111 " model vdw 2.224 3.350 nonbonded pdb=" O HIS I1224 " pdb=" N6 SAM I1501 " model vdw 2.263 2.520 nonbonded pdb=" O ALA I1212 " pdb=" NH2 ARG I1220 " model vdw 2.279 2.520 ... (remaining 115214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 27 through 121) } ncs_group { reference = chain 'E' selection = (chain 'M' and resid 37 through 134) } 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=0.93 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 3.190 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 51.000 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 : 0.007 0.054 15785 Z= 0.384 Angle : 0.759 8.857 22761 Z= 0.450 Chirality : 0.043 0.224 2572 Planarity : 0.005 0.054 1729 Dihedral : 27.070 169.684 6769 Min Nonbonded Distance : 1.478 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.05 % Favored : 91.85 % Rotamer: Outliers : 0.96 % Allowed : 5.17 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -5.47 (0.18), residues: 969 helix: -3.46 (0.15), residues: 511 sheet: -3.13 (0.83), residues: 16 loop : -3.84 (0.20), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP I1157 HIS 0.007 0.001 HIS H 79 PHE 0.015 0.002 PHE F 61 TYR 0.018 0.002 TYR I1261 ARG 0.005 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: D 31 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7960 (mmtt) REVERT: D 83 ARG cc_start: 0.8347 (mmt-90) cc_final: 0.8133 (mmt180) REVERT: G 112 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8769 (mm110) REVERT: H 39 TYR cc_start: 0.8324 (t80) cc_final: 0.8115 (t80) outliers start: 8 outliers final: 3 residues processed: 133 average time/residue: 0.4220 time to fit residues: 72.8345 Evaluate side-chains 115 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 30.0000 chunk 116 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN F 25 ASN G 31 HIS H 60 ASN I1135 GLN I1137 GLN I1192 HIS ** I1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN I1233 GLN I1238 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15785 Z= 0.217 Angle : 0.605 9.177 22761 Z= 0.353 Chirality : 0.037 0.158 2572 Planarity : 0.004 0.054 1729 Dihedral : 29.805 171.072 4819 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.20 % Allowed : 8.17 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.21), residues: 969 helix: -2.58 (0.19), residues: 509 sheet: -2.52 (1.00), residues: 16 loop : -3.31 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I1157 HIS 0.005 0.001 HIS H 79 PHE 0.015 0.002 PHE I1170 TYR 0.014 0.001 TYR I1261 ARG 0.004 0.000 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: M 133 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8019 (mt-10) REVERT: D 31 LYS cc_start: 0.8162 (mtmp) cc_final: 0.7739 (mtpp) REVERT: D 56 MET cc_start: 0.8557 (tpp) cc_final: 0.8015 (mmt) REVERT: D 83 ARG cc_start: 0.8394 (mmt-90) cc_final: 0.8160 (mmt180) REVERT: E 123 ASP cc_start: 0.9017 (m-30) cc_final: 0.8655 (m-30) REVERT: F 84 MET cc_start: 0.8338 (mmm) cc_final: 0.7893 (mmt) REVERT: G 112 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8792 (mm110) outliers start: 10 outliers final: 8 residues processed: 117 average time/residue: 0.3854 time to fit residues: 60.3045 Evaluate side-chains 116 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1087 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** I1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15785 Z= 0.298 Angle : 0.625 7.789 22761 Z= 0.362 Chirality : 0.039 0.152 2572 Planarity : 0.005 0.057 1729 Dihedral : 29.831 171.262 4809 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.32 % Allowed : 10.34 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.22), residues: 969 helix: -2.38 (0.19), residues: 510 sheet: -1.82 (1.12), residues: 16 loop : -3.09 (0.23), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I1157 HIS 0.006 0.001 HIS H 79 PHE 0.013 0.002 PHE H 67 TYR 0.015 0.002 TYR I1261 ARG 0.005 0.000 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7694 (mt-10) REVERT: D 31 LYS cc_start: 0.8210 (mtmp) cc_final: 0.7891 (mtpt) REVERT: D 83 ARG cc_start: 0.8376 (mmt-90) cc_final: 0.8138 (mmt180) REVERT: E 123 ASP cc_start: 0.9024 (m-30) cc_final: 0.8684 (m-30) REVERT: F 84 MET cc_start: 0.8431 (mmm) cc_final: 0.7835 (mmt) REVERT: G 112 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8823 (mm110) outliers start: 11 outliers final: 8 residues processed: 118 average time/residue: 0.3668 time to fit residues: 58.2495 Evaluate side-chains 117 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 60 optimal weight: 0.0570 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 0.0570 chunk 33 optimal weight: 6.9990 overall best weight: 1.4020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15785 Z= 0.183 Angle : 0.580 7.764 22761 Z= 0.342 Chirality : 0.036 0.151 2572 Planarity : 0.004 0.056 1729 Dihedral : 29.795 171.010 4809 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.92 % Allowed : 10.10 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.68 (0.22), residues: 969 helix: -2.04 (0.20), residues: 502 sheet: -1.26 (1.17), residues: 16 loop : -2.95 (0.23), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I1157 HIS 0.005 0.001 HIS H 79 PHE 0.027 0.001 PHE I1170 TYR 0.012 0.001 TYR I1261 ARG 0.004 0.000 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7643 (mt-10) REVERT: M 133 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8045 (mt-10) REVERT: D 31 LYS cc_start: 0.8157 (mtmp) cc_final: 0.7865 (mtpt) REVERT: D 83 ARG cc_start: 0.8393 (mmt-90) cc_final: 0.8150 (mmt180) REVERT: E 123 ASP cc_start: 0.8996 (m-30) cc_final: 0.8651 (m-30) REVERT: F 84 MET cc_start: 0.8447 (mmm) cc_final: 0.7906 (mmt) REVERT: G 112 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8817 (mm110) outliers start: 16 outliers final: 13 residues processed: 128 average time/residue: 0.3629 time to fit residues: 63.2640 Evaluate side-chains 123 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1229 ASN Chi-restraints excluded: chain I residue 1251 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 chunk 85 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1106 ASN I1137 GLN ** I1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15785 Z= 0.392 Angle : 0.671 11.029 22761 Z= 0.383 Chirality : 0.042 0.156 2572 Planarity : 0.005 0.058 1729 Dihedral : 29.863 171.056 4809 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.16 % Allowed : 12.14 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.84 (0.22), residues: 969 helix: -2.23 (0.20), residues: 500 sheet: -0.86 (1.20), residues: 18 loop : -2.98 (0.23), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP I1157 HIS 0.006 0.001 HIS H 79 PHE 0.015 0.002 PHE F 61 TYR 0.019 0.002 TYR I1261 ARG 0.005 0.001 ARG M 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7705 (mt-10) REVERT: D 31 LYS cc_start: 0.8358 (mtmp) cc_final: 0.8023 (mtpt) REVERT: D 83 ARG cc_start: 0.8401 (mmt-90) cc_final: 0.8172 (mmt180) REVERT: E 73 GLU cc_start: 0.8230 (tm-30) cc_final: 0.8027 (tm-30) REVERT: E 123 ASP cc_start: 0.9005 (m-30) cc_final: 0.8651 (m-30) REVERT: F 84 MET cc_start: 0.8519 (mmm) cc_final: 0.7932 (mmt) REVERT: G 112 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8837 (mm110) REVERT: H 54 LYS cc_start: 0.8850 (tptt) cc_final: 0.8580 (tptm) outliers start: 18 outliers final: 14 residues processed: 128 average time/residue: 0.3742 time to fit residues: 64.9454 Evaluate side-chains 127 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1106 ASN Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1204 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1106 ASN I1137 GLN ** I1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 15785 Z= 0.192 Angle : 0.585 10.582 22761 Z= 0.344 Chirality : 0.036 0.145 2572 Planarity : 0.005 0.063 1729 Dihedral : 29.773 171.236 4809 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.44 % Allowed : 12.62 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.40 (0.23), residues: 969 helix: -1.84 (0.21), residues: 496 sheet: -0.86 (1.22), residues: 16 loop : -2.78 (0.24), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I1157 HIS 0.004 0.000 HIS H 79 PHE 0.009 0.001 PHE D 67 TYR 0.013 0.001 TYR I1261 ARG 0.005 0.000 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7671 (mt-10) REVERT: M 133 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8044 (mt-10) REVERT: D 31 LYS cc_start: 0.8309 (mtmp) cc_final: 0.7994 (mtpt) REVERT: D 83 ARG cc_start: 0.8390 (mmt-90) cc_final: 0.8150 (mmt180) REVERT: E 73 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7895 (tt0) REVERT: E 123 ASP cc_start: 0.8970 (m-30) cc_final: 0.8622 (m-30) REVERT: F 84 MET cc_start: 0.8468 (mmm) cc_final: 0.7940 (mmt) REVERT: G 112 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8829 (mm110) outliers start: 12 outliers final: 11 residues processed: 125 average time/residue: 0.3691 time to fit residues: 62.1528 Evaluate side-chains 128 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1229 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 40.0000 chunk 104 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15785 Z= 0.306 Angle : 0.622 9.066 22761 Z= 0.359 Chirality : 0.039 0.145 2572 Planarity : 0.005 0.058 1729 Dihedral : 29.799 171.711 4809 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.80 % Allowed : 12.98 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.49 (0.23), residues: 969 helix: -1.96 (0.21), residues: 497 sheet: -0.67 (1.31), residues: 16 loop : -2.78 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP I1157 HIS 0.005 0.001 HIS H 79 PHE 0.013 0.002 PHE F 61 TYR 0.017 0.002 TYR I1261 ARG 0.005 0.000 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7708 (mt-10) REVERT: M 133 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8041 (mt-10) REVERT: D 83 ARG cc_start: 0.8378 (mmt-90) cc_final: 0.8143 (mmt180) REVERT: E 73 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7975 (tt0) REVERT: E 123 ASP cc_start: 0.9029 (m-30) cc_final: 0.8685 (m-30) REVERT: F 84 MET cc_start: 0.8499 (mmm) cc_final: 0.7961 (mmt) REVERT: G 112 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8835 (mm110) outliers start: 15 outliers final: 13 residues processed: 127 average time/residue: 0.3635 time to fit residues: 62.8035 Evaluate side-chains 128 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1229 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15785 Z= 0.186 Angle : 0.571 9.238 22761 Z= 0.335 Chirality : 0.036 0.141 2572 Planarity : 0.004 0.055 1729 Dihedral : 29.745 171.937 4809 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.44 % Allowed : 13.34 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.22 (0.23), residues: 969 helix: -1.71 (0.21), residues: 494 sheet: -0.48 (1.33), residues: 16 loop : -2.67 (0.24), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I1157 HIS 0.003 0.000 HIS H 79 PHE 0.010 0.001 PHE D 67 TYR 0.012 0.001 TYR I1261 ARG 0.006 0.000 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7661 (mt-10) REVERT: M 133 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7983 (mt-10) REVERT: D 31 LYS cc_start: 0.8333 (mtmp) cc_final: 0.8019 (mtpt) REVERT: D 83 ARG cc_start: 0.8360 (mmt-90) cc_final: 0.8125 (mmt180) REVERT: E 73 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7901 (tt0) REVERT: E 123 ASP cc_start: 0.8973 (m-30) cc_final: 0.8629 (m-30) REVERT: G 112 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8827 (mm110) outliers start: 12 outliers final: 11 residues processed: 123 average time/residue: 0.3591 time to fit residues: 59.9935 Evaluate side-chains 126 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1204 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 40.0000 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 121 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15785 Z= 0.164 Angle : 0.562 9.193 22761 Z= 0.331 Chirality : 0.035 0.144 2572 Planarity : 0.004 0.055 1729 Dihedral : 29.732 172.118 4809 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.32 % Allowed : 13.70 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.10 (0.23), residues: 969 helix: -1.61 (0.21), residues: 494 sheet: -0.41 (1.31), residues: 16 loop : -2.61 (0.24), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I1157 HIS 0.004 0.001 HIS H 79 PHE 0.010 0.001 PHE D 67 TYR 0.012 0.001 TYR I1261 ARG 0.006 0.000 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7647 (mt-10) REVERT: M 133 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7991 (mt-10) REVERT: D 31 LYS cc_start: 0.8322 (mtmp) cc_final: 0.8004 (mtpt) REVERT: D 83 ARG cc_start: 0.8385 (mmt-90) cc_final: 0.8149 (mmt180) REVERT: E 73 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7899 (tt0) REVERT: E 123 ASP cc_start: 0.8968 (m-30) cc_final: 0.8625 (m-30) REVERT: G 112 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8818 (mm110) outliers start: 11 outliers final: 10 residues processed: 124 average time/residue: 0.3724 time to fit residues: 62.2474 Evaluate side-chains 125 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1204 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 40.0000 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 0.0870 chunk 80 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 overall best weight: 2.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15785 Z= 0.240 Angle : 0.580 8.701 22761 Z= 0.337 Chirality : 0.036 0.143 2572 Planarity : 0.004 0.056 1729 Dihedral : 29.717 172.781 4809 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.20 % Allowed : 13.70 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.12 (0.23), residues: 969 helix: -1.66 (0.21), residues: 493 sheet: -0.47 (1.25), residues: 18 loop : -2.60 (0.24), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I1157 HIS 0.004 0.001 HIS H 79 PHE 0.010 0.001 PHE F 61 TYR 0.014 0.001 TYR I1261 ARG 0.006 0.000 ARG M 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.394 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7674 (mt-10) REVERT: M 133 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8061 (mt-10) REVERT: D 31 LYS cc_start: 0.8338 (mtmp) cc_final: 0.8019 (mtpt) REVERT: D 83 ARG cc_start: 0.8343 (mmt-90) cc_final: 0.8111 (mmt180) REVERT: E 73 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7978 (tt0) REVERT: E 123 ASP cc_start: 0.8970 (m-30) cc_final: 0.8621 (m-30) REVERT: G 112 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8779 (mm110) outliers start: 10 outliers final: 10 residues processed: 120 average time/residue: 0.3660 time to fit residues: 60.1069 Evaluate side-chains 123 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1204 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 104 optimal weight: 30.0000 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.183038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.139803 restraints weight = 17120.744| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.19 r_work: 0.2958 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15785 Z= 0.233 Angle : 0.578 8.684 22761 Z= 0.336 Chirality : 0.036 0.144 2572 Planarity : 0.004 0.056 1729 Dihedral : 29.717 172.786 4809 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.32 % Allowed : 13.58 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.11 (0.23), residues: 969 helix: -1.65 (0.21), residues: 493 sheet: -0.46 (1.26), residues: 18 loop : -2.59 (0.24), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I1157 HIS 0.004 0.001 HIS H 79 PHE 0.010 0.001 PHE D 67 TYR 0.014 0.001 TYR I1261 ARG 0.006 0.000 ARG M 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2772.75 seconds wall clock time: 50 minutes 55.77 seconds (3055.77 seconds total)