Starting phenix.real_space_refine on Wed Mar 20 07:04:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cro_30453/03_2024/7cro_30453_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cro_30453/03_2024/7cro_30453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cro_30453/03_2024/7cro_30453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cro_30453/03_2024/7cro_30453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cro_30453/03_2024/7cro_30453_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cro_30453/03_2024/7cro_30453_updated.pdb" } resolution = 3.75 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= 0.001 sd= 0.006 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 12063 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 30 5.16 5 C 8235 2.51 5 N 2762 2.21 5 O 3431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M GLU 59": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "I GLU 1040": "OE1" <-> "OE2" Residue "I ARG 1060": "NH1" <-> "NH2" Residue "I GLU 1101": "OE1" <-> "OE2" Residue "I ARG 1138": "NH1" <-> "NH2" Residue "I ARG 1160": "NH1" <-> "NH2" Residue "I GLU 1174": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14797 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: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1761 Unusual residues: {' ZN': 3} Classifications: {'peptide': 220, 'undetermined': 3} Link IDs: {'PTRANS': 13, 'TRANS': 206, None: 3} Not linked: pdbres="SAM I1401 " pdbres=" ZN I1402 " Not linked: pdbres=" ZN I1402 " pdbres=" ZN I1403 " Not linked: pdbres=" ZN I1403 " pdbres=" ZN I1404 " Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13279 SG CYS I1016 59.525 92.667 71.375 1.00 74.39 S ATOM 13293 SG CYS I1018 62.061 90.974 69.713 1.00 91.22 S ATOM 13354 SG CYS I1026 59.637 93.550 67.996 1.00 85.87 S ATOM 13398 SG CYS I1032 58.228 89.896 69.399 1.00 68.52 S ATOM 13475 SG CYS I1041 54.903 93.115 69.256 1.00 88.65 S ATOM 13556 SG CYS I1052 56.026 94.118 66.143 1.00 84.65 S ATOM 14669 SG CYS I1191 35.820 63.419 55.974 1.00110.31 S ATOM 14686 SG CYS I1193 37.494 65.438 53.715 1.00103.59 S ATOM 14715 SG CYS I1198 38.607 61.460 51.915 1.00105.52 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N SAM I1401 " occ=0.93 ... (25 atoms not shown) pdb=" O4' SAM I1401 " occ=0.93 Time building chain proxies: 8.46, per 1000 atoms: 0.57 Number of scatterers: 14797 At special positions: 0 Unit cell: (136.08, 151.2, 173.88, 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 30 16.00 P 336 15.00 O 3431 8.00 N 2762 7.00 C 8235 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: 7.17 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I1402 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1026 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1032 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1018 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1016 " pdb=" ZN I1403 " pdb="ZN ZN I1403 " - pdb=" SG CYS I1041 " pdb="ZN ZN I1403 " - pdb=" SG CYS I1052 " pdb=" ZN I1404 " pdb="ZN ZN I1404 " - pdb=" SG CYS I1191 " pdb="ZN ZN I1404 " - pdb=" SG CYS I1193 " pdb="ZN ZN I1404 " - pdb=" SG CYS I1198 " Number of angles added : 6 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 3 sheets defined 43.3% alpha, 1.5% beta 114 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 6.78 Creating SS restraints... Processing helix chain 'M' and resid 46 through 54 removed outlier: 3.844A pdb=" N GLU M 50 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE M 51 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 76 removed outlier: 3.616A pdb=" N LEU M 70 " --> pdb=" O PRO M 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL M 71 " --> pdb=" O PHE M 67 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG M 72 " --> pdb=" O GLN M 68 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 91 Processing helix chain 'M' and resid 93 through 103 removed outlier: 3.822A pdb=" N GLU M 97 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 113 removed outlier: 3.750A pdb=" N CYS M 110 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 131 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.779A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 removed outlier: 4.507A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 76 removed outlier: 4.698A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 removed outlier: 4.229A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 37 removed outlier: 4.094A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.541A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 61 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 66 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 87 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 44 removed outlier: 3.754A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 80 removed outlier: 3.654A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 96 removed outlier: 3.842A pdb=" N THR D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 119 removed outlier: 4.096A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.944A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 113 removed outlier: 3.761A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 131 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 41 Processing helix chain 'F' and resid 54 through 76 removed outlier: 4.176A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 93 removed outlier: 3.916A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 removed outlier: 4.435A 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: 3.920A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 55 removed outlier: 3.772A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 73 removed outlier: 4.177A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 87 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 43 removed outlier: 3.501A pdb=" N LEU H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 38 through 43' Processing helix chain 'H' and resid 53 through 80 removed outlier: 3.982A pdb=" N SER H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N MET H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA H 74 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 98 removed outlier: 4.026A pdb=" N ARG H 96 " --> pdb=" O GLN H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 120 removed outlier: 3.635A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYR H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1112 removed outlier: 3.514A pdb=" N ALA I1104 " --> pdb=" O GLU I1100 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA I1109 " --> pdb=" O ARG I1105 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU I1111 " --> pdb=" O LYS I1107 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASN I1112 " --> pdb=" O HIS I1108 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'I' and resid 1148 through 1150 removed outlier: 3.873A pdb=" N GLU I1149 " --> pdb=" O PHE I1164 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 1153 through 1155 Processing sheet with id= C, first strand: chain 'I' and resid 1119 through 1123 removed outlier: 3.682A pdb=" N LEU I1120 " --> pdb=" O ILE I1128 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE I1122 " --> pdb=" O ARG I1126 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARG I1126 " --> pdb=" O ILE I1122 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 570 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 300 hydrogen bonds 600 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 7.60 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: 2912 1.33 - 1.45: 4975 1.45 - 1.57: 7155 1.57 - 1.69: 670 1.69 - 1.81: 43 Bond restraints: 15755 Sorted by residual: bond pdb=" CA LYS I 998 " pdb=" C LYS I 998 " ideal model delta sigma weight residual 1.524 1.487 0.037 1.26e-02 6.30e+03 8.73e+00 bond pdb=" C2 SAM I1401 " pdb=" N3 SAM I1401 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" C8 SAM I1401 " pdb=" N7 SAM I1401 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" C2 SAM I1401 " pdb=" N1 SAM I1401 " ideal model delta sigma weight residual 1.329 1.380 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" N LYS I 998 " pdb=" CA LYS I 998 " ideal model delta sigma weight residual 1.457 1.424 0.033 1.41e-02 5.03e+03 5.54e+00 ... (remaining 15750 not shown) Histogram of bond angle deviations from ideal: 97.46 - 104.77: 1393 104.77 - 112.08: 8639 112.08 - 119.39: 4841 119.39 - 126.70: 6865 126.70 - 134.01: 990 Bond angle restraints: 22728 Sorted by residual: angle pdb=" O3' DA A 28 " pdb=" C3' DA A 28 " pdb=" C2' DA A 28 " ideal model delta sigma weight residual 111.50 100.64 10.86 1.50e+00 4.44e-01 5.24e+01 angle pdb=" N LYS I 995 " pdb=" CA LYS I 995 " pdb=" C LYS I 995 " ideal model delta sigma weight residual 111.03 116.38 -5.35 1.11e+00 8.12e-01 2.32e+01 angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 111.67 115.92 -4.25 9.20e-01 1.18e+00 2.13e+01 angle pdb=" N LYS I1124 " pdb=" CA LYS I1124 " pdb=" C LYS I1124 " ideal model delta sigma weight residual 109.96 103.55 6.41 1.50e+00 4.44e-01 1.83e+01 angle pdb=" C4' DA A 28 " pdb=" C3' DA A 28 " pdb=" O3' DA A 28 " ideal model delta sigma weight residual 110.00 115.85 -5.85 1.50e+00 4.44e-01 1.52e+01 ... (remaining 22723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 6949 34.78 - 69.56: 1614 69.56 - 104.34: 33 104.34 - 139.11: 0 139.11 - 173.89: 1 Dihedral angle restraints: 8597 sinusoidal: 5709 harmonic: 2888 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 180.00 155.32 24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" N ASP I1125 " pdb=" C ASP I1125 " pdb=" CA ASP I1125 " pdb=" CB ASP I1125 " ideal model delta harmonic sigma weight residual 122.80 133.29 -10.49 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" CA TYR I1062 " pdb=" C TYR I1062 " pdb=" N PRO I1063 " pdb=" CA PRO I1063 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 8594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2408 0.074 - 0.149: 153 0.149 - 0.223: 6 0.223 - 0.297: 0 0.297 - 0.371: 1 Chirality restraints: 2568 Sorted by residual: chirality pdb=" CA ASP I1125 " pdb=" N ASP I1125 " pdb=" C ASP I1125 " pdb=" CB ASP I1125 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA SER G 113 " pdb=" N SER G 113 " pdb=" C SER G 113 " pdb=" CB SER G 113 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA ILE I1127 " pdb=" N ILE I1127 " pdb=" C ILE I1127 " pdb=" CB ILE I1127 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.24e-01 ... (remaining 2565 not shown) Planarity restraints: 1723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS I 998 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO I 999 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO I 999 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 999 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE I1097 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C ILE I1097 " -0.045 2.00e-02 2.50e+03 pdb=" O ILE I1097 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP I1098 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG A 141 " 0.036 2.00e-02 2.50e+03 1.50e-02 6.75e+00 pdb=" N9 DG A 141 " -0.034 2.00e-02 2.50e+03 pdb=" C8 DG A 141 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DG A 141 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG A 141 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG A 141 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG A 141 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DG A 141 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG A 141 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG A 141 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG A 141 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG A 141 " -0.002 2.00e-02 2.50e+03 ... (remaining 1720 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 3 2.12 - 2.81: 3734 2.81 - 3.51: 18148 3.51 - 4.20: 36296 4.20 - 4.90: 54710 Nonbonded interactions: 112891 Sorted by model distance: nonbonded pdb=" NH2 ARG I1126 " pdb=" OG1 THR I1159 " model vdw 1.421 2.520 nonbonded pdb=" CE1 HIS M 39 " pdb=" OE1 GLU I1149 " model vdw 1.762 3.260 nonbonded pdb=" O CYS I1198 " pdb="ZN ZN I1404 " model vdw 2.086 2.230 nonbonded pdb=" O GLU I1091 " pdb=" OG SER I1137 " model vdw 2.154 2.440 nonbonded pdb=" O TYR F 51 " pdb=" NH1 ARG F 55 " model vdw 2.162 2.520 ... (remaining 112886 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' and (resid 10 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and (resid 10 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 117 or (resid 118 and (name N or n \ ame CA or name C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 27 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 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 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: 1.570 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: 3.560 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 48.540 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.006 0.057 15755 Z= 0.345 Angle : 0.738 10.857 22728 Z= 0.454 Chirality : 0.041 0.371 2568 Planarity : 0.005 0.071 1723 Dihedral : 27.717 173.892 6737 Min Nonbonded Distance : 1.421 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.45 % Allowed : 5.08 % Favored : 93.47 % Cbeta Deviations : 0.11 % 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: -5.38 (0.19), residues: 966 helix: -3.15 (0.17), residues: 483 sheet: -4.20 (0.78), residues: 25 loop : -4.05 (0.21), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I1075 HIS 0.005 0.001 HIS M 39 PHE 0.010 0.002 PHE I1039 TYR 0.020 0.002 TYR H 118 ARG 0.003 0.000 ARG I1035 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.211 Fit side-chains REVERT: B 84 MET cc_start: 0.8368 (mmm) cc_final: 0.8150 (mmt) REVERT: D 90 GLU cc_start: 0.8160 (mp0) cc_final: 0.7465 (mp0) REVERT: E 73 GLU cc_start: 0.8006 (tt0) cc_final: 0.7650 (tt0) REVERT: E 106 ASP cc_start: 0.8539 (m-30) cc_final: 0.8321 (m-30) REVERT: E 123 ASP cc_start: 0.8151 (m-30) cc_final: 0.7753 (m-30) REVERT: F 91 LYS cc_start: 0.8912 (tttm) cc_final: 0.8661 (tptt) REVERT: G 118 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.6396 (tptp) outliers start: 12 outliers final: 5 residues processed: 133 average time/residue: 0.4062 time to fit residues: 70.4201 Evaluate side-chains 99 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain I residue 1006 TYR Chi-restraints excluded: chain I residue 1102 CYS Chi-restraints excluded: chain I residue 1103 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 50.0000 chunk 116 optimal weight: 6.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 39 HIS B 25 ASN E 125 GLN F 25 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 993 HIS I 997 ASN I1034 ASN ** I1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15755 Z= 0.299 Angle : 0.616 5.910 22728 Z= 0.358 Chirality : 0.038 0.135 2568 Planarity : 0.004 0.052 1723 Dihedral : 30.575 174.569 4810 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.06 % Allowed : 11.00 % Favored : 86.94 % 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: -4.26 (0.22), residues: 966 helix: -2.11 (0.21), residues: 477 sheet: -3.10 (0.74), residues: 32 loop : -3.66 (0.23), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I1075 HIS 0.005 0.001 HIS M 39 PHE 0.015 0.001 PHE I1088 TYR 0.022 0.002 TYR I1062 ARG 0.004 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8367 (tt0) cc_final: 0.8119 (tt0) REVERT: E 68 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8454 (pt0) REVERT: E 73 GLU cc_start: 0.7986 (tt0) cc_final: 0.7605 (tt0) REVERT: E 106 ASP cc_start: 0.8561 (m-30) cc_final: 0.8295 (m-30) REVERT: E 123 ASP cc_start: 0.8156 (m-30) cc_final: 0.7628 (m-30) REVERT: F 91 LYS cc_start: 0.8843 (tttm) cc_final: 0.8631 (tptt) outliers start: 17 outliers final: 10 residues processed: 98 average time/residue: 0.3754 time to fit residues: 50.6689 Evaluate side-chains 96 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 1089 VAL Chi-restraints excluded: chain I residue 1102 CYS Chi-restraints excluded: chain I residue 1193 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 30.0000 chunk 125 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 115 optimal weight: 0.0170 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15755 Z= 0.290 Angle : 0.598 6.353 22728 Z= 0.348 Chirality : 0.038 0.132 2568 Planarity : 0.004 0.043 1723 Dihedral : 30.511 174.561 4800 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.18 % Allowed : 14.51 % Favored : 83.31 % 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: -3.83 (0.23), residues: 966 helix: -1.73 (0.22), residues: 469 sheet: -2.76 (0.81), residues: 28 loop : -3.47 (0.24), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I1075 HIS 0.004 0.001 HIS H 46 PHE 0.009 0.001 PHE I1039 TYR 0.023 0.002 TYR I1062 ARG 0.003 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: D 56 MET cc_start: 0.8807 (tpt) cc_final: 0.8405 (tpt) REVERT: E 68 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8450 (pt0) REVERT: E 106 ASP cc_start: 0.8512 (m-30) cc_final: 0.8262 (m-30) REVERT: F 91 LYS cc_start: 0.8864 (tttm) cc_final: 0.8635 (tptt) REVERT: G 92 GLU cc_start: 0.7799 (mp0) cc_final: 0.7486 (mp0) outliers start: 18 outliers final: 14 residues processed: 97 average time/residue: 0.3237 time to fit residues: 43.6366 Evaluate side-chains 98 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 1089 VAL Chi-restraints excluded: chain I residue 1102 CYS Chi-restraints excluded: chain I residue 1193 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.0870 chunk 87 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 33 optimal weight: 0.4980 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15755 Z= 0.153 Angle : 0.513 5.351 22728 Z= 0.305 Chirality : 0.034 0.182 2568 Planarity : 0.003 0.038 1723 Dihedral : 30.148 174.537 4800 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.21 % Allowed : 16.69 % Favored : 82.10 % 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: -3.06 (0.25), residues: 966 helix: -1.03 (0.24), residues: 471 sheet: -2.70 (0.81), residues: 28 loop : -3.14 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I1075 HIS 0.004 0.001 HIS I1110 PHE 0.011 0.001 PHE I1117 TYR 0.014 0.001 TYR I1062 ARG 0.003 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 1.127 Fit side-chains REVERT: E 106 ASP cc_start: 0.8330 (m-30) cc_final: 0.8027 (m-30) REVERT: F 91 LYS cc_start: 0.8783 (tttm) cc_final: 0.8565 (tptp) REVERT: H 56 MET cc_start: 0.7332 (tpt) cc_final: 0.7041 (tpt) REVERT: I 1119 MET cc_start: 0.6361 (mmt) cc_final: 0.6054 (mmt) REVERT: I 1143 SER cc_start: 0.8579 (t) cc_final: 0.7944 (m) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.3349 time to fit residues: 47.9768 Evaluate side-chains 96 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 1006 TYR Chi-restraints excluded: chain I residue 1089 VAL Chi-restraints excluded: chain I residue 1193 CYS 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: 6.9990 chunk 1 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 105 optimal weight: 40.0000 chunk 85 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 110 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 15755 Z= 0.510 Angle : 0.722 8.794 22728 Z= 0.410 Chirality : 0.044 0.166 2568 Planarity : 0.005 0.045 1723 Dihedral : 30.801 173.524 4798 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 3.26 % Allowed : 18.50 % Favored : 78.23 % 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: -3.69 (0.23), residues: 966 helix: -1.69 (0.22), residues: 466 sheet: -2.78 (0.81), residues: 28 loop : -3.30 (0.24), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I1075 HIS 0.007 0.002 HIS B 75 PHE 0.014 0.002 PHE I1039 TYR 0.023 0.002 TYR H 118 ARG 0.007 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 1.217 Fit side-chains REVERT: M 39 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.7133 (m-70) REVERT: D 77 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9066 (tt) REVERT: E 68 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8479 (pt0) REVERT: E 123 ASP cc_start: 0.8214 (m-30) cc_final: 0.7601 (m-30) REVERT: F 91 LYS cc_start: 0.8896 (tttm) cc_final: 0.8355 (tptp) outliers start: 27 outliers final: 18 residues processed: 107 average time/residue: 0.3071 time to fit residues: 46.0362 Evaluate side-chains 105 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 1006 TYR Chi-restraints excluded: chain I residue 1089 VAL Chi-restraints excluded: chain I residue 1193 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15755 Z= 0.200 Angle : 0.547 7.066 22728 Z= 0.322 Chirality : 0.035 0.146 2568 Planarity : 0.004 0.035 1723 Dihedral : 30.358 175.689 4798 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.81 % Allowed : 20.07 % Favored : 78.11 % 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: -3.16 (0.24), residues: 966 helix: -1.13 (0.23), residues: 466 sheet: -2.60 (0.84), residues: 28 loop : -3.15 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I1075 HIS 0.005 0.001 HIS I1110 PHE 0.009 0.001 PHE I1117 TYR 0.017 0.001 TYR I1062 ARG 0.013 0.000 ARG I1192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 1.341 Fit side-chains REVERT: D 77 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9005 (tt) REVERT: F 25 ASN cc_start: 0.8332 (m-40) cc_final: 0.8048 (m110) REVERT: F 91 LYS cc_start: 0.8810 (tttm) cc_final: 0.8546 (tptp) REVERT: G 92 GLU cc_start: 0.8009 (mp0) cc_final: 0.7796 (mp0) REVERT: I 1119 MET cc_start: 0.6490 (mmt) cc_final: 0.5863 (mmt) outliers start: 15 outliers final: 10 residues processed: 96 average time/residue: 0.3318 time to fit residues: 45.1313 Evaluate side-chains 93 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 1006 TYR Chi-restraints excluded: chain I residue 1089 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 overall best weight: 4.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 15755 Z= 0.331 Angle : 0.606 7.601 22728 Z= 0.352 Chirality : 0.038 0.131 2568 Planarity : 0.004 0.036 1723 Dihedral : 30.509 174.249 4798 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 2.78 % Allowed : 19.47 % Favored : 77.75 % 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: -3.28 (0.24), residues: 966 helix: -1.28 (0.23), residues: 462 sheet: -2.67 (0.83), residues: 28 loop : -3.14 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I1075 HIS 0.004 0.001 HIS M 39 PHE 0.010 0.001 PHE H 67 TYR 0.018 0.002 TYR I1062 ARG 0.005 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 1.032 Fit side-chains REVERT: D 77 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9085 (tt) REVERT: E 68 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8475 (pt0) REVERT: E 123 ASP cc_start: 0.8132 (m-30) cc_final: 0.7580 (m-30) REVERT: F 25 ASN cc_start: 0.8412 (m-40) cc_final: 0.8184 (m110) REVERT: F 91 LYS cc_start: 0.8850 (tttm) cc_final: 0.8352 (tptp) REVERT: G 92 GLU cc_start: 0.7997 (mp0) cc_final: 0.7746 (mp0) REVERT: H 60 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8663 (t0) REVERT: I 1064 GLU cc_start: 0.5652 (OUTLIER) cc_final: 0.5392 (pm20) REVERT: I 1119 MET cc_start: 0.6546 (mmt) cc_final: 0.5997 (mmt) outliers start: 23 outliers final: 15 residues processed: 101 average time/residue: 0.2990 time to fit residues: 42.7696 Evaluate side-chains 102 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 1006 TYR Chi-restraints excluded: chain I residue 1064 GLU Chi-restraints excluded: chain I residue 1089 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 60 ASN ** I1142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15755 Z= 0.150 Angle : 0.517 6.248 22728 Z= 0.305 Chirality : 0.033 0.138 2568 Planarity : 0.003 0.031 1723 Dihedral : 30.132 175.079 4798 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.33 % Allowed : 20.80 % Favored : 77.87 % 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: -2.55 (0.25), residues: 966 helix: -0.68 (0.24), residues: 464 sheet: -2.40 (0.89), residues: 28 loop : -2.76 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I1075 HIS 0.006 0.001 HIS I1110 PHE 0.028 0.001 PHE I1117 TYR 0.017 0.001 TYR I1062 ARG 0.003 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: F 25 ASN cc_start: 0.8291 (m-40) cc_final: 0.8000 (m110) REVERT: F 91 LYS cc_start: 0.8788 (tttm) cc_final: 0.8579 (tptp) REVERT: H 60 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8401 (t0) REVERT: I 1143 SER cc_start: 0.8649 (t) cc_final: 0.8009 (m) outliers start: 11 outliers final: 7 residues processed: 98 average time/residue: 0.3164 time to fit residues: 43.2627 Evaluate side-chains 93 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1089 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 7.9990 chunk 107 optimal weight: 0.2980 chunk 114 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 108 optimal weight: 0.2980 chunk 75 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15755 Z= 0.144 Angle : 0.508 7.019 22728 Z= 0.301 Chirality : 0.033 0.138 2568 Planarity : 0.003 0.031 1723 Dihedral : 30.126 173.361 4798 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.60 % Allowed : 22.25 % Favored : 77.15 % 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: -2.07 (0.26), residues: 966 helix: -0.26 (0.24), residues: 466 sheet: -2.30 (0.94), residues: 28 loop : -2.54 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I1075 HIS 0.006 0.001 HIS I1110 PHE 0.029 0.001 PHE I1117 TYR 0.018 0.001 TYR I1062 ARG 0.004 0.000 ARG I1192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: F 25 ASN cc_start: 0.8297 (m-40) cc_final: 0.7975 (m110) REVERT: F 91 LYS cc_start: 0.8802 (tttm) cc_final: 0.8578 (tptp) REVERT: I 1143 SER cc_start: 0.8529 (t) cc_final: 0.7853 (m) outliers start: 5 outliers final: 4 residues processed: 93 average time/residue: 0.3469 time to fit residues: 44.5503 Evaluate side-chains 91 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 1089 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 50.0000 chunk 57 optimal weight: 0.0010 chunk 84 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 10 optimal weight: 0.0870 chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 108 optimal weight: 0.0670 overall best weight: 2.4306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN I1112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15755 Z= 0.206 Angle : 0.535 7.094 22728 Z= 0.313 Chirality : 0.034 0.133 2568 Planarity : 0.004 0.056 1723 Dihedral : 30.170 174.694 4798 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.45 % Allowed : 21.77 % Favored : 76.78 % 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: -2.21 (0.25), residues: 966 helix: -0.38 (0.24), residues: 466 sheet: -2.32 (0.93), residues: 28 loop : -2.62 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I1075 HIS 0.005 0.001 HIS I1110 PHE 0.033 0.001 PHE I1088 TYR 0.016 0.001 TYR I1062 ARG 0.012 0.000 ARG I1138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: E 68 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8385 (pt0) REVERT: F 25 ASN cc_start: 0.8350 (m-40) cc_final: 0.8042 (m110) REVERT: F 91 LYS cc_start: 0.8803 (tttm) cc_final: 0.8318 (tptp) REVERT: G 92 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7628 (mm-30) REVERT: H 60 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8453 (t0) REVERT: I 1143 SER cc_start: 0.8492 (t) cc_final: 0.7807 (m) outliers start: 12 outliers final: 9 residues processed: 93 average time/residue: 0.3171 time to fit residues: 41.6726 Evaluate side-chains 97 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1089 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 14 optimal weight: 0.0030 chunk 28 optimal weight: 0.0870 chunk 101 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.0570 chunk 89 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 overall best weight: 0.6088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.134577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.093200 restraints weight = 35631.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092113 restraints weight = 37879.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.092209 restraints weight = 40230.179| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15755 Z= 0.147 Angle : 0.512 10.056 22728 Z= 0.300 Chirality : 0.032 0.138 2568 Planarity : 0.004 0.040 1723 Dihedral : 30.014 175.347 4798 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.48 % Allowed : 22.61 % Favored : 76.90 % 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: -1.88 (0.26), residues: 966 helix: -0.14 (0.24), residues: 466 sheet: -2.25 (0.95), residues: 28 loop : -2.40 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I1075 HIS 0.006 0.001 HIS I1110 PHE 0.034 0.001 PHE I1088 TYR 0.017 0.001 TYR F 51 ARG 0.010 0.000 ARG I1138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2080.13 seconds wall clock time: 38 minutes 37.67 seconds (2317.67 seconds total)