Starting phenix.real_space_refine on Mon Sep 30 01:11:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/09_2024/6ddd_7867_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/09_2024/6ddd_7867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/09_2024/6ddd_7867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/09_2024/6ddd_7867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/09_2024/6ddd_7867_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/09_2024/6ddd_7867_trim.cif" } resolution = 3.1 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 2747 5.49 5 S 54 5.16 5 Cl 2 4.86 5 C 38916 2.51 5 N 14700 2.21 5 O 22698 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.82s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 79118 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 915 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "B" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2094 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Chain: "C" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "D" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "F" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 711 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "G" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 730 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "H" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 592 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "J" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 463 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "K" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 472 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Chain: "M" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 432 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "N" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 397 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "O" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 382 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "P" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Q" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "R" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "S" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1318 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain breaks: 2 Chain: "V" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1138 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "W" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 850 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain breaks: 1 Chain: "X" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 938 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain breaks: 2 Chain: "Y" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "Z" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 902 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain breaks: 1 Chain: "a" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 583 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain breaks: 2 Chain: "1" Number of atoms: 56747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2646, 56747 Inner-chain residues flagged as termini: ['pdbres=" A 11459 "', 'pdbres=" G 11556 "'] Classifications: {'RNA': 2646} Modifications used: {'5*END': 3, 'rna2p_pur': 267, 'rna2p_pyr': 131, 'rna3p_pur': 1257, 'rna3p_pyr': 991} Link IDs: {'rna2p': 398, 'rna3p': 2247} Chain breaks: 9 Chain: "2" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2214 Classifications: {'RNA': 104} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 46, 'rna3p_pyr': 44} Link IDs: {'rna2p': 14, 'rna3p': 89} Chain: "1" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'G6V': 1} Classifications: {'undetermined': 1} Time building chain proxies: 32.76, per 1000 atoms: 0.41 Number of scatterers: 79118 At special positions: 0 Unit cell: (192.92, 232.14, 186.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 54 16.00 P 2747 15.00 F 1 9.00 O 22698 8.00 N 14700 7.00 C 38916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 43 " distance=2.03 Simple disulfide: pdb=" SG CYS O 12 " - pdb=" SG CYS O 36 " distance=2.04 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 27 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 14.01 Conformation dependent library (CDL) restraints added in 2.9 seconds 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4674 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 41 sheets defined 24.3% alpha, 19.1% beta 853 base pairs and 1482 stacking pairs defined. Time for finding SS restraints: 28.97 Creating SS restraints... Processing helix chain 'A' and resid 99 through 105 removed outlier: 3.512A pdb=" N LEU A 102 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 105 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 removed outlier: 3.665A pdb=" N LEU B 34 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 removed outlier: 4.332A pdb=" N GLU B 201 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 264 through 268 removed outlier: 4.212A pdb=" N LYS B 268 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.598A pdb=" N ARG C 13 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 31 through 70 removed outlier: 4.226A pdb=" N GLN C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 76 through 83 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 102 through 115 removed outlier: 3.540A pdb=" N PHE C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 28 through 39 Processing helix chain 'E' and resid 43 through 62 Processing helix chain 'F' and resid 34 through 46 removed outlier: 3.700A pdb=" N VAL F 38 " --> pdb=" O ASN F 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 24 Processing helix chain 'H' and resid 45 through 53 Processing helix chain 'K' and resid 10 through 23 removed outlier: 3.546A pdb=" N ILE K 14 " --> pdb=" O THR K 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU K 23 " --> pdb=" O LYS K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 35 Processing helix chain 'K' and resid 40 through 60 removed outlier: 3.959A pdb=" N ARG K 44 " --> pdb=" O THR K 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 80 removed outlier: 4.018A pdb=" N ALA L 80 " --> pdb=" O HIS L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 110 Processing helix chain 'L' and resid 128 through 135 removed outlier: 4.036A pdb=" N LYS L 132 " --> pdb=" O GLN L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 26 Processing helix chain 'M' and resid 41 through 50 removed outlier: 3.556A pdb=" N GLY M 45 " --> pdb=" O PRO M 41 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE M 47 " --> pdb=" O ILE M 43 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS M 49 " --> pdb=" O GLY M 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 17 Processing helix chain 'N' and resid 18 through 20 No H-bonds generated for 'chain 'N' and resid 18 through 20' Processing helix chain 'P' and resid 9 through 18 Processing helix chain 'P' and resid 18 through 24 removed outlier: 3.516A pdb=" N ARG P 22 " --> pdb=" O GLY P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 39 Processing helix chain 'Q' and resid 37 through 44 removed outlier: 3.538A pdb=" N LEU Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 58 Processing helix chain 'R' and resid 29 through 32 Processing helix chain 'S' and resid 29 through 44 removed outlier: 4.152A pdb=" N GLU S 35 " --> pdb=" O SER S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 119 Processing helix chain 'S' and resid 135 through 146 removed outlier: 3.829A pdb=" N LEU S 146 " --> pdb=" O VAL S 142 " (cutoff:3.500A) Processing helix chain 'S' and resid 163 through 168 Processing helix chain 'S' and resid 179 through 181 No H-bonds generated for 'chain 'S' and resid 179 through 181' Processing helix chain 'S' and resid 183 through 189 Processing helix chain 'S' and resid 195 through 206 removed outlier: 3.646A pdb=" N LYS S 200 " --> pdb=" O GLU S 196 " (cutoff:3.500A) Processing helix chain 'V' and resid 25 through 39 removed outlier: 4.253A pdb=" N GLU V 32 " --> pdb=" O ARG V 28 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 63 removed outlier: 4.095A pdb=" N ILE V 63 " --> pdb=" O ALA V 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 97 removed outlier: 3.609A pdb=" N ARG V 95 " --> pdb=" O GLY V 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 108 removed outlier: 4.048A pdb=" N GLU V 103 " --> pdb=" O GLU V 99 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 121 removed outlier: 3.732A pdb=" N LYS V 118 " --> pdb=" O ARG V 114 " (cutoff:3.500A) Processing helix chain 'V' and resid 133 through 137 removed outlier: 3.758A pdb=" N GLN V 137 " --> pdb=" O ALA V 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 104 through 109 Processing helix chain 'W' and resid 111 through 118 removed outlier: 3.959A pdb=" N LEU W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 54 removed outlier: 4.170A pdb=" N GLY X 53 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN X 54 " --> pdb=" O GLU X 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 50 through 54' Processing helix chain 'X' and resid 56 through 60 removed outlier: 3.512A pdb=" N ARG X 59 " --> pdb=" O PRO X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 92 through 99 Processing helix chain 'X' and resid 129 through 136 Processing helix chain 'Y' and resid 44 through 58 removed outlier: 4.318A pdb=" N SER Y 49 " --> pdb=" O ARG Y 45 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE Y 52 " --> pdb=" O GLU Y 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 110 through 122 Processing helix chain 'Z' and resid 9 through 28 Processing helix chain 'Z' and resid 34 through 42 removed outlier: 4.038A pdb=" N SER Z 42 " --> pdb=" O LYS Z 38 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 54 removed outlier: 3.817A pdb=" N LEU Z 50 " --> pdb=" O LYS Z 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 64 Processing helix chain 'Z' and resid 81 through 87 Processing helix chain 'Z' and resid 87 through 93 removed outlier: 4.016A pdb=" N GLU Z 91 " --> pdb=" O GLY Z 87 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG Z 92 " --> pdb=" O GLU Z 88 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR Z 93 " --> pdb=" O ILE Z 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 87 through 93' Processing helix chain 'a' and resid 7 through 17 removed outlier: 3.672A pdb=" N LEU a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS a 13 " --> pdb=" O LYS a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 90 removed outlier: 6.724A pdb=" N HIS A 31 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE A 86 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG A 29 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL A 88 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 27 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 32 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N GLU A 46 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE A 66 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR A 62 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ARG A 52 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A 60 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 82 removed outlier: 5.585A pdb=" N VAL B 78 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL B 95 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 129 through 131 Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 175 removed outlier: 6.737A pdb=" N VAL B 181 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.697A pdb=" N ILE D 4 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 19 through 23 removed outlier: 6.820A pdb=" N TYR D 92 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLN D 65 " --> pdb=" O TYR D 92 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS D 94 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR D 59 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 71 through 77 removed outlier: 4.252A pdb=" N SER D 82 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 10 removed outlier: 3.566A pdb=" N THR E 9 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER E 101 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER E 108 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL E 71 " --> pdb=" O SER E 108 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 82 through 87 Processing sheet with id=AB2, first strand: chain 'F' and resid 7 through 10 removed outlier: 4.030A pdb=" N ARG F 76 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG F 75 " --> pdb=" O TYR F 58 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LYS F 83 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL F 50 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 20 through 21 removed outlier: 3.540A pdb=" N GLY G 21 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU G 70 " --> pdb=" O THR G 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 26 through 27 Processing sheet with id=AB5, first strand: chain 'G' and resid 40 through 44 Processing sheet with id=AB6, first strand: chain 'G' and resid 81 through 84 Processing sheet with id=AB7, first strand: chain 'H' and resid 39 through 44 removed outlier: 11.074A pdb=" N LYS H 26 " --> pdb=" O GLN H 85 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N THR H 87 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ILE H 86 " --> pdb=" O ASP H 80 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ASP H 80 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS H 88 " --> pdb=" O GLN H 78 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP H 76 " --> pdb=" O ASP H 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 64 through 65 removed outlier: 3.758A pdb=" N VAL H 65 " --> pdb=" O LYS H 68 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 44 through 46 removed outlier: 6.338A pdb=" N LEU I 67 " --> pdb=" O LEU I 45 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 54 through 55 removed outlier: 6.890A pdb=" N TYR I 54 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N VAL I 89 " --> pdb=" O TYR I 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 13 through 17 Processing sheet with id=AC3, first strand: chain 'J' and resid 33 through 40 removed outlier: 3.735A pdb=" N VAL J 40 " --> pdb=" O LYS J 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 5 through 16 removed outlier: 5.475A pdb=" N LYS L 9 " --> pdb=" O GLU L 29 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU L 29 " --> pdb=" O LYS L 9 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL L 194 " --> pdb=" O VAL L 188 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL L 188 " --> pdb=" O VAL L 194 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU L 196 " --> pdb=" O VAL L 186 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU L 184 " --> pdb=" O LYS L 198 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N THR L 179 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY L 120 " --> pdb=" O THR L 179 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLN L 181 " --> pdb=" O VAL L 118 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL L 118 " --> pdb=" O GLN L 181 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL L 121 " --> pdb=" O LEU L 208 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU L 208 " --> pdb=" O VAL L 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 38 through 39 Processing sheet with id=AC6, first strand: chain 'L' and resid 54 through 55 Processing sheet with id=AC7, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AC8, first strand: chain 'N' and resid 27 through 29 Processing sheet with id=AC9, first strand: chain 'O' and resid 3 through 8 removed outlier: 3.906A pdb=" N TYR O 17 " --> pdb=" O LEU O 7 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 32 through 36 Processing sheet with id=AD2, first strand: chain 'Q' and resid 15 through 16 removed outlier: 3.677A pdb=" N LYS Q 15 " --> pdb=" O LYS Q 23 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 2 through 3 removed outlier: 6.755A pdb=" N LYS R 2 " --> pdb=" O ARG R 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'R' and resid 15 through 19 Processing sheet with id=AD5, first strand: chain 'S' and resid 174 through 177 removed outlier: 6.176A pdb=" N VAL S 152 " --> pdb=" O GLN S 174 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR S 176 " --> pdb=" O VAL S 152 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL S 154 " --> pdb=" O THR S 176 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU S 153 " --> pdb=" O VAL S 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'V' and resid 123 through 125 removed outlier: 6.642A pdb=" N VAL V 55 " --> pdb=" O PHE V 124 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR V 17 " --> pdb=" O ILE V 56 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE V 58 " --> pdb=" O TYR V 17 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE V 19 " --> pdb=" O ILE V 58 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP V 16 " --> pdb=" O GLU V 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'V' and resid 74 through 78 Processing sheet with id=AD8, first strand: chain 'W' and resid 7 through 9 removed outlier: 6.682A pdb=" N GLU W 18 " --> pdb=" O LYS W 44 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL W 40 " --> pdb=" O ILE W 22 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL W 24 " --> pdb=" O VAL W 38 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N VAL W 38 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS W 59 " --> pdb=" O ILE W 87 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA W 83 " --> pdb=" O VAL W 63 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 75 through 77 removed outlier: 3.876A pdb=" N LYS X 127 " --> pdb=" O ILE X 109 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE X 111 " --> pdb=" O LYS X 127 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 32 through 36 Processing sheet with id=AE2, first strand: chain 'Y' and resid 40 through 43 removed outlier: 5.212A pdb=" N VAL Y 90 " --> pdb=" O LYS Y 76 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LYS Y 76 " --> pdb=" O VAL Y 90 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY Y 92 " --> pdb=" O TYR Y 74 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR Y 72 " --> pdb=" O ILE Y 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Y' and resid 63 through 66 Processing sheet with id=AE4, first strand: chain 'Z' and resid 29 through 33 removed outlier: 6.416A pdb=" N ILE Z 118 " --> pdb=" O LYS Z 105 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LYS Z 105 " --> pdb=" O ILE Z 118 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU Z 120 " --> pdb=" O ILE Z 103 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE Z 103 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'a' and resid 30 through 34 removed outlier: 7.627A pdb=" N ALA a 42 " --> pdb=" O GLN a 55 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLN a 55 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE a 44 " --> pdb=" O LEU a 53 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2129 hydrogen bonds 3406 hydrogen bond angles 0 basepair planarities 853 basepair parallelities 1482 stacking parallelities Total time for adding SS restraints: 136.52 Time building geometry restraints manager: 17.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 7356 1.31 - 1.44: 39475 1.44 - 1.57: 34023 1.57 - 1.71: 5484 1.71 - 1.84: 96 Bond restraints: 86434 Sorted by residual: bond pdb=" C ARG M 20 " pdb=" O ARG M 20 " ideal model delta sigma weight residual 1.237 1.174 0.062 1.17e-02 7.31e+03 2.83e+01 bond pdb=" C1' U 2 68 " pdb=" N1 U 2 68 " ideal model delta sigma weight residual 1.480 1.556 -0.076 1.50e-02 4.44e+03 2.57e+01 bond pdb=" C10 G6V 13001 " pdb=" C20 G6V 13001 " ideal model delta sigma weight residual 1.511 1.598 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C30 G6V 13001 " pdb=" N29 G6V 13001 " ideal model delta sigma weight residual 1.336 1.420 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C31 G6V 13001 " pdb="CL33 G6V 13001 " ideal model delta sigma weight residual 1.758 1.838 -0.080 2.00e-02 2.50e+03 1.60e+01 ... (remaining 86429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.54: 129965 4.54 - 9.09: 243 9.09 - 13.63: 22 13.63 - 18.17: 2 18.17 - 22.72: 1 Bond angle restraints: 130233 Sorted by residual: angle pdb=" O2' G 11931 " pdb=" C2' G 11931 " pdb=" C1' G 11931 " ideal model delta sigma weight residual 108.40 85.68 22.72 1.50e+00 4.44e-01 2.29e+02 angle pdb=" C4' A 2 20 " pdb=" C3' A 2 20 " pdb=" O3' A 2 20 " ideal model delta sigma weight residual 113.00 126.89 -13.89 1.50e+00 4.44e-01 8.57e+01 angle pdb=" O2' A 2 81 " pdb=" C2' A 2 81 " pdb=" C1' A 2 81 " ideal model delta sigma weight residual 108.40 94.63 13.77 1.50e+00 4.44e-01 8.43e+01 angle pdb=" O2' G 2 80 " pdb=" C2' G 2 80 " pdb=" C1' G 2 80 " ideal model delta sigma weight residual 108.40 95.20 13.20 1.50e+00 4.44e-01 7.75e+01 angle pdb=" O2' G 2 19 " pdb=" C2' G 2 19 " pdb=" C1' G 2 19 " ideal model delta sigma weight residual 108.40 95.24 13.16 1.50e+00 4.44e-01 7.70e+01 ... (remaining 130228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 48398 35.98 - 71.95: 6189 71.95 - 107.93: 624 107.93 - 143.91: 15 143.91 - 179.88: 34 Dihedral angle restraints: 55260 sinusoidal: 47994 harmonic: 7266 Sorted by residual: dihedral pdb=" O4' U 12361 " pdb=" C1' U 12361 " pdb=" N1 U 12361 " pdb=" C2 U 12361 " ideal model delta sinusoidal sigma weight residual 200.00 20.12 179.88 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 11781 " pdb=" C1' C 11781 " pdb=" N1 C 11781 " pdb=" C2 C 11781 " ideal model delta sinusoidal sigma weight residual 200.00 21.71 178.29 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 12417 " pdb=" C1' U 12417 " pdb=" N1 U 12417 " pdb=" C2 U 12417 " ideal model delta sinusoidal sigma weight residual -160.00 17.68 -177.68 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 55257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 15535 0.085 - 0.169: 1126 0.169 - 0.254: 114 0.254 - 0.338: 15 0.338 - 0.422: 2 Chirality restraints: 16792 Sorted by residual: chirality pdb=" C3' A 2 20 " pdb=" C4' A 2 20 " pdb=" O3' A 2 20 " pdb=" C2' A 2 20 " both_signs ideal model delta sigma weight residual False -2.48 -2.05 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C3' U 2 89 " pdb=" C4' U 2 89 " pdb=" O3' U 2 89 " pdb=" C2' U 2 89 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C1' A 1 125 " pdb=" O4' A 1 125 " pdb=" C2' A 1 125 " pdb=" N9 A 1 125 " both_signs ideal model delta sigma weight residual False 2.46 2.13 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 16789 not shown) Planarity restraints: 6241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 11955 " 0.060 2.00e-02 2.50e+03 3.47e-02 3.32e+01 pdb=" N9 A 11955 " -0.096 2.00e-02 2.50e+03 pdb=" C8 A 11955 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 11955 " 0.018 2.00e-02 2.50e+03 pdb=" C5 A 11955 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A 11955 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A 11955 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A 11955 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A 11955 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A 11955 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A 11955 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 20 " -0.052 2.00e-02 2.50e+03 3.10e-02 2.65e+01 pdb=" N9 A 2 20 " 0.086 2.00e-02 2.50e+03 pdb=" C8 A 2 20 " -0.007 2.00e-02 2.50e+03 pdb=" N7 A 2 20 " -0.008 2.00e-02 2.50e+03 pdb=" C5 A 2 20 " -0.017 2.00e-02 2.50e+03 pdb=" C6 A 2 20 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A 2 20 " -0.001 2.00e-02 2.50e+03 pdb=" N1 A 2 20 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A 2 20 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A 2 20 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A 2 20 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 82 " 0.045 2.00e-02 2.50e+03 2.49e-02 1.71e+01 pdb=" N9 A 2 82 " -0.068 2.00e-02 2.50e+03 pdb=" C8 A 2 82 " 0.009 2.00e-02 2.50e+03 pdb=" N7 A 2 82 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A 2 82 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A 2 82 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A 2 82 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A 2 82 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A 2 82 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A 2 82 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A 2 82 " -0.002 2.00e-02 2.50e+03 ... (remaining 6238 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 1153 2.58 - 3.16: 60873 3.16 - 3.74: 148348 3.74 - 4.32: 223068 4.32 - 4.90: 298154 Nonbonded interactions: 731596 Sorted by model distance: nonbonded pdb=" OP1 U 11063 " pdb=" O2' U 11079 " model vdw 1.998 3.040 nonbonded pdb=" OH TYR F 58 " pdb=" OP2 U 11377 " model vdw 2.003 3.040 nonbonded pdb=" OP2 A 11070 " pdb=" O2' C 11178 " model vdw 2.016 3.040 nonbonded pdb=" O2' C 11423 " pdb=" O2 U 11512 " model vdw 2.027 3.040 nonbonded pdb=" O2' A 12060 " pdb=" OP2 G 12062 " model vdw 2.032 3.040 ... (remaining 731591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 2.320 Check model and map are aligned: 0.460 Set scattering table: 0.570 Process input model: 251.390 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 261.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.008 0.106 86434 Z= 0.490 Angle : 0.854 22.717 130233 Z= 0.455 Chirality : 0.048 0.422 16792 Planarity : 0.006 0.068 6241 Dihedral : 23.613 179.882 50577 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.31 % 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: -4.62 (0.13), residues: 2500 helix: -2.93 (0.16), residues: 596 sheet: -3.09 (0.19), residues: 501 loop : -3.19 (0.13), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.005 TRP B 213 HIS 0.015 0.003 HIS E 102 PHE 0.044 0.003 PHE L 127 TYR 0.036 0.003 TYR F 58 ARG 0.017 0.002 ARG X 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 747 time to evaluate : 3.167 Fit side-chains REVERT: C 91 ASN cc_start: 0.8567 (p0) cc_final: 0.8304 (p0) REVERT: D 69 LYS cc_start: 0.7445 (mmtt) cc_final: 0.7214 (mmmt) REVERT: D 78 ARG cc_start: 0.7848 (ptt180) cc_final: 0.7551 (ptt180) REVERT: E 59 GLU cc_start: 0.5888 (pp20) cc_final: 0.5660 (pp20) REVERT: F 12 ILE cc_start: 0.8380 (pt) cc_final: 0.8054 (tp) REVERT: H 68 LYS cc_start: 0.6803 (pttp) cc_final: 0.6126 (mptt) REVERT: I 61 ARG cc_start: 0.8741 (ppt-90) cc_final: 0.8424 (ptt90) REVERT: I 90 TYR cc_start: 0.6906 (m-10) cc_final: 0.6690 (m-80) REVERT: K 54 LYS cc_start: 0.8812 (mmmm) cc_final: 0.8533 (mmmt) REVERT: L 8 ARG cc_start: 0.8465 (ttm-80) cc_final: 0.8159 (ttm170) REVERT: O 21 LYS cc_start: 0.7738 (pttt) cc_final: 0.7045 (ttmt) REVERT: P 7 GLN cc_start: 0.8889 (mm110) cc_final: 0.8678 (mm-40) REVERT: S 77 THR cc_start: 0.8687 (p) cc_final: 0.8427 (t) REVERT: S 179 GLN cc_start: 0.7139 (tp40) cc_final: 0.6786 (mm-40) REVERT: V 121 LYS cc_start: 0.8124 (ptpt) cc_final: 0.7772 (pttt) REVERT: W 59 LYS cc_start: 0.8241 (mttt) cc_final: 0.7851 (mtmt) REVERT: X 38 GLN cc_start: 0.8429 (tt0) cc_final: 0.8158 (tt0) REVERT: X 73 GLU cc_start: 0.6135 (pt0) cc_final: 0.5849 (pt0) REVERT: Y 26 TYR cc_start: 0.8029 (m-80) cc_final: 0.7770 (m-10) REVERT: Y 48 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6277 (mm-30) REVERT: Z 79 GLN cc_start: 0.7070 (mt0) cc_final: 0.6693 (mt0) REVERT: a 8 ASN cc_start: 0.7242 (t0) cc_final: 0.7020 (t0) outliers start: 1 outliers final: 1 residues processed: 748 average time/residue: 0.9318 time to fit residues: 1117.5803 Evaluate side-chains 543 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 542 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 18 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 439 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 407 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 247 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 472 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN B 128 ASN B 199 GLN B 200 HIS C 37 GLN C 38 GLN E 28 ASN E 40 ASN E 57 ASN E 60 HIS E 61 ASN F 34 ASN F 57 ASN G 76 ASN H 38 ASN H 88 HIS L 128 GLN L 134 HIS L 143 HIS L 146 HIS L 182 ASN L 192 ASN M 52 HIS N 45 ASN O 4 ASN O 25 ASN O 26 ASN ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 HIS Q 31 HIS S 67 GLN S 75 GLN S 162 ASN S 169 ASN V 3 GLN V 8 ASN V 68 ASN V 119 GLN V 137 GLN X 17 ASN Y 13 HIS Y 35 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN a 39 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 86434 Z= 0.259 Angle : 0.658 10.734 130233 Z= 0.339 Chirality : 0.039 0.280 16792 Planarity : 0.005 0.063 6241 Dihedral : 23.930 179.899 45377 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.44 % Allowed : 10.08 % Favored : 86.48 % 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 (0.14), residues: 2500 helix: -1.69 (0.19), residues: 606 sheet: -2.53 (0.21), residues: 478 loop : -2.58 (0.14), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 213 HIS 0.009 0.001 HIS B 53 PHE 0.022 0.002 PHE Y 32 TYR 0.020 0.002 TYR F 58 ARG 0.008 0.001 ARG X 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 565 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 GLN cc_start: 0.8103 (mt0) cc_final: 0.7861 (mt0) REVERT: D 69 LYS cc_start: 0.7524 (mmtt) cc_final: 0.7188 (mmmt) REVERT: I 33 ARG cc_start: 0.8925 (mmt180) cc_final: 0.8724 (mmt-90) REVERT: L 8 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.8264 (ttm170) REVERT: L 162 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7363 (ppt-90) REVERT: S 179 GLN cc_start: 0.7035 (tp40) cc_final: 0.6766 (mm-40) REVERT: S 186 ILE cc_start: 0.8896 (mt) cc_final: 0.8677 (mt) REVERT: V 121 LYS cc_start: 0.8158 (ptpt) cc_final: 0.7947 (mttt) REVERT: X 73 GLU cc_start: 0.6148 (pt0) cc_final: 0.5893 (pt0) REVERT: Y 48 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6186 (mm-30) REVERT: a 96 ARG cc_start: 0.7688 (ptt90) cc_final: 0.7484 (ptt90) outliers start: 74 outliers final: 48 residues processed: 596 average time/residue: 0.8641 time to fit residues: 852.3603 Evaluate side-chains 545 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 496 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain V residue 3 GLN Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 112 ASP Chi-restraints excluded: chain Z residue 119 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 262 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 393 optimal weight: 6.9990 chunk 321 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 473 optimal weight: 8.9990 chunk 511 optimal weight: 10.0000 chunk 421 optimal weight: 10.0000 chunk 469 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 379 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN C 81 ASN D 65 GLN F 54 ASN K 31 GLN L 33 ASN L 192 ASN L 200 ASN O 4 ASN O 45 HIS S 67 GLN V 8 ASN V 68 ASN V 81 HIS V 137 GLN Y 35 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.096 86434 Z= 0.521 Angle : 0.861 12.178 130233 Z= 0.428 Chirality : 0.049 0.322 16792 Planarity : 0.007 0.081 6241 Dihedral : 24.039 179.517 45377 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 5.11 % Allowed : 13.56 % Favored : 81.33 % 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: -3.31 (0.15), residues: 2500 helix: -1.57 (0.19), residues: 615 sheet: -2.33 (0.21), residues: 486 loop : -2.48 (0.14), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 213 HIS 0.011 0.002 HIS E 102 PHE 0.026 0.003 PHE Y 32 TYR 0.030 0.003 TYR F 58 ARG 0.009 0.001 ARG S 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 481 time to evaluate : 3.161 Fit side-chains REVERT: D 69 LYS cc_start: 0.7651 (mmtt) cc_final: 0.7313 (mmmt) REVERT: G 57 LEU cc_start: 0.5937 (OUTLIER) cc_final: 0.5667 (tp) REVERT: K 60 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7939 (mtt-85) REVERT: L 32 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: L 103 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7247 (pt0) REVERT: L 162 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7402 (ppt-90) REVERT: N 7 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8382 (ptt180) REVERT: Q 52 LYS cc_start: 0.8057 (ptpt) cc_final: 0.7726 (mmtm) REVERT: V 137 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.6976 (mp-120) REVERT: W 120 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7156 (pt0) REVERT: Y 48 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6285 (mm-30) REVERT: Z 44 VAL cc_start: 0.9346 (p) cc_final: 0.9015 (t) outliers start: 110 outliers final: 86 residues processed: 541 average time/residue: 0.8384 time to fit residues: 750.0088 Evaluate side-chains 552 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 459 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 7 ARG Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain O residue 4 ASN Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain V residue 3 GLN Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 120 GLU Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 112 ASP Chi-restraints excluded: chain Z residue 119 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 92 ILE Chi-restraints excluded: chain a residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 467 optimal weight: 4.9990 chunk 355 optimal weight: 7.9990 chunk 245 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 225 optimal weight: 0.8980 chunk 317 optimal weight: 4.9990 chunk 474 optimal weight: 7.9990 chunk 502 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 449 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 HIS C 81 ASN L 66 ASN L 200 ASN O 4 ASN Q 7 HIS V 3 GLN V 8 ASN V 68 ASN V 137 GLN Y 35 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 86434 Z= 0.241 Angle : 0.631 11.178 130233 Z= 0.326 Chirality : 0.038 0.294 16792 Planarity : 0.005 0.056 6241 Dihedral : 23.814 179.306 45377 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.60 % Allowed : 15.61 % Favored : 79.80 % 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: -2.77 (0.15), residues: 2500 helix: -1.00 (0.20), residues: 612 sheet: -1.99 (0.22), residues: 477 loop : -2.21 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 213 HIS 0.005 0.001 HIS E 102 PHE 0.018 0.002 PHE S 139 TYR 0.015 0.002 TYR F 58 ARG 0.006 0.001 ARG S 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 497 time to evaluate : 3.088 Fit side-chains revert: symmetry clash REVERT: G 16 ASP cc_start: 0.6328 (m-30) cc_final: 0.6057 (m-30) REVERT: G 57 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5834 (tp) REVERT: L 32 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: L 103 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7059 (pt0) REVERT: L 162 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7420 (ppt-90) REVERT: Q 52 LYS cc_start: 0.8036 (ptpt) cc_final: 0.7684 (mmtm) REVERT: W 120 GLU cc_start: 0.7416 (pp20) cc_final: 0.7208 (pt0) REVERT: Y 5 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.6914 (ttpp) REVERT: Y 58 MET cc_start: 0.7329 (mtm) cc_final: 0.7090 (mtm) REVERT: Z 118 ILE cc_start: 0.9016 (mt) cc_final: 0.8658 (mt) outliers start: 99 outliers final: 70 residues processed: 550 average time/residue: 0.8464 time to fit residues: 767.5044 Evaluate side-chains 552 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 477 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain V residue 3 GLN Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain W residue 113 LYS Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 418 optimal weight: 9.9990 chunk 285 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 374 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 428 optimal weight: 8.9990 chunk 347 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 451 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 HIS C 29 HIS E 97 ASN L 66 ASN L 200 ASN M 40 ASN P 17 HIS S 162 ASN V 68 ASN V 137 GLN ** W 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 86434 Z= 0.414 Angle : 0.759 12.243 130233 Z= 0.382 Chirality : 0.044 0.309 16792 Planarity : 0.006 0.067 6241 Dihedral : 23.879 179.871 45377 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 5.85 % Allowed : 16.12 % Favored : 78.03 % 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: -2.73 (0.15), residues: 2500 helix: -1.02 (0.20), residues: 610 sheet: -1.89 (0.22), residues: 484 loop : -2.18 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 250 HIS 0.008 0.001 HIS E 102 PHE 0.020 0.002 PHE S 139 TYR 0.021 0.002 TYR V 141 ARG 0.009 0.001 ARG S 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 466 time to evaluate : 3.090 Fit side-chains revert: symmetry clash REVERT: B 180 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7153 (tt0) REVERT: E 66 THR cc_start: 0.8237 (p) cc_final: 0.7839 (m) REVERT: G 57 LEU cc_start: 0.5917 (OUTLIER) cc_final: 0.5710 (tp) REVERT: L 103 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: L 162 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7273 (ppt-90) REVERT: L 210 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: O 32 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7962 (mpp) REVERT: Q 52 LYS cc_start: 0.8075 (ptpt) cc_final: 0.7694 (mmtm) REVERT: V 13 GLU cc_start: 0.7155 (pm20) cc_final: 0.6897 (pm20) REVERT: W 120 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7225 (pt0) REVERT: Z 44 VAL cc_start: 0.9291 (p) cc_final: 0.9002 (t) outliers start: 126 outliers final: 93 residues processed: 539 average time/residue: 0.8337 time to fit residues: 749.2741 Evaluate side-chains 562 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 462 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 34 ARG Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 60 GLN Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain V residue 3 GLN Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 87 SER Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain W residue 113 LYS Chi-restraints excluded: chain W residue 120 GLU Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 119 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 169 optimal weight: 0.8980 chunk 452 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 295 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 503 optimal weight: 5.9990 chunk 417 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 264 optimal weight: 7.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN H 85 GLN L 76 HIS O 4 ASN Q 7 HIS V 3 GLN V 8 ASN V 68 ASN W 13 ASN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 86434 Z= 0.178 Angle : 0.582 10.913 130233 Z= 0.302 Chirality : 0.035 0.290 16792 Planarity : 0.005 0.049 6241 Dihedral : 23.678 179.544 45377 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.64 % Allowed : 18.35 % Favored : 77.01 % 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: -2.26 (0.16), residues: 2500 helix: -0.52 (0.21), residues: 604 sheet: -1.62 (0.23), residues: 491 loop : -1.93 (0.15), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 250 HIS 0.005 0.001 HIS C 29 PHE 0.018 0.001 PHE S 139 TYR 0.012 0.001 TYR V 141 ARG 0.004 0.000 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 493 time to evaluate : 3.113 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8170 (ttmt) REVERT: B 180 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6900 (tt0) REVERT: B 187 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7782 (m) REVERT: E 66 THR cc_start: 0.8165 (p) cc_final: 0.7751 (m) REVERT: G 16 ASP cc_start: 0.6279 (m-30) cc_final: 0.6020 (m-30) REVERT: G 57 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5843 (tp) REVERT: J 37 ARG cc_start: 0.7353 (ttm110) cc_final: 0.6932 (ttm170) REVERT: L 162 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7429 (ppt-90) REVERT: P 15 LYS cc_start: 0.8660 (mmtp) cc_final: 0.8360 (mmtt) REVERT: Q 52 LYS cc_start: 0.8040 (ptpt) cc_final: 0.7609 (mmtm) REVERT: Y 5 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7017 (ttpp) REVERT: Z 115 GLU cc_start: 0.7650 (tp30) cc_final: 0.7427 (tp30) REVERT: Z 118 ILE cc_start: 0.8919 (mt) cc_final: 0.8654 (mt) outliers start: 100 outliers final: 68 residues processed: 545 average time/residue: 0.8553 time to fit residues: 775.1809 Evaluate side-chains 544 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 470 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain O residue 4 ASN Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain X residue 99 SER Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 485 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 286 optimal weight: 8.9990 chunk 367 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 423 optimal weight: 10.0000 chunk 280 optimal weight: 10.0000 chunk 501 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN C 37 GLN C 81 ASN H 85 GLN L 66 ASN L 103 GLN L 200 ASN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 ASN V 8 ASN V 59 ASN V 68 ASN V 137 GLN W 3 GLN X 4 HIS ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.114 86434 Z= 0.615 Angle : 0.939 12.712 130233 Z= 0.460 Chirality : 0.052 0.342 16792 Planarity : 0.007 0.093 6241 Dihedral : 23.968 179.377 45376 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 5.85 % Allowed : 18.25 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.15), residues: 2500 helix: -1.09 (0.20), residues: 611 sheet: -1.78 (0.22), residues: 492 loop : -2.24 (0.15), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP J 29 HIS 0.011 0.002 HIS E 102 PHE 0.026 0.003 PHE L 91 TYR 0.023 0.003 TYR Z 93 ARG 0.011 0.001 ARG S 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 458 time to evaluate : 3.114 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8687 (ttmt) REVERT: A 112 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7735 (mm) REVERT: B 180 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: C 70 ARG cc_start: 0.7846 (mmt90) cc_final: 0.7597 (mmt-90) REVERT: E 66 THR cc_start: 0.8298 (p) cc_final: 0.7925 (m) REVERT: G 57 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5810 (tp) REVERT: I 35 ASP cc_start: 0.7939 (t70) cc_final: 0.7606 (t0) REVERT: L 162 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7293 (ppt-90) REVERT: L 210 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: O 32 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7910 (mpp) REVERT: Q 52 LYS cc_start: 0.8049 (ptpt) cc_final: 0.7623 (mmtm) REVERT: S 158 ASN cc_start: 0.5597 (OUTLIER) cc_final: 0.5340 (t0) REVERT: Z 44 VAL cc_start: 0.9356 (p) cc_final: 0.9059 (t) outliers start: 126 outliers final: 100 residues processed: 535 average time/residue: 0.8402 time to fit residues: 749.9043 Evaluate side-chains 557 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 449 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain O residue 4 ASN Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 60 GLN Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 158 ASN Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 87 SER Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain W residue 113 LYS Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 40 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 310 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 299 optimal weight: 4.9990 chunk 150 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 318 optimal weight: 8.9990 chunk 341 optimal weight: 0.6980 chunk 247 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 393 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN V 3 GLN V 8 ASN V 68 ASN V 137 GLN ** W 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 86434 Z= 0.171 Angle : 0.589 9.815 130233 Z= 0.306 Chirality : 0.036 0.292 16792 Planarity : 0.005 0.051 6241 Dihedral : 23.693 179.608 45376 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.18 % Allowed : 19.37 % Favored : 76.45 % 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: -2.22 (0.16), residues: 2500 helix: -0.50 (0.21), residues: 603 sheet: -1.52 (0.23), residues: 486 loop : -1.93 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 250 HIS 0.006 0.001 HIS C 29 PHE 0.017 0.001 PHE S 139 TYR 0.024 0.001 TYR V 141 ARG 0.006 0.000 ARG L 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 479 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8080 (ttmt) REVERT: B 180 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6973 (tt0) REVERT: D 85 LYS cc_start: 0.8853 (ttmm) cc_final: 0.8631 (ttpp) REVERT: E 66 THR cc_start: 0.8328 (p) cc_final: 0.7939 (m) REVERT: G 60 GLU cc_start: 0.6797 (mp0) cc_final: 0.6567 (mp0) REVERT: J 37 ARG cc_start: 0.7346 (ttm110) cc_final: 0.7117 (ttm110) REVERT: L 162 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7414 (ppt-90) REVERT: P 15 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8401 (mmtt) REVERT: Q 52 LYS cc_start: 0.7975 (ptpt) cc_final: 0.7543 (mmtm) REVERT: W 9 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7451 (mmtt) REVERT: W 87 ILE cc_start: 0.8663 (mm) cc_final: 0.8295 (pt) outliers start: 90 outliers final: 72 residues processed: 530 average time/residue: 0.8412 time to fit residues: 739.1583 Evaluate side-chains 542 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 467 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 34 ARG Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain V residue 3 GLN Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain X residue 99 SER Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 455 optimal weight: 10.9990 chunk 480 optimal weight: 7.9990 chunk 438 optimal weight: 6.9990 chunk 467 optimal weight: 7.9990 chunk 281 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 366 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 422 optimal weight: 10.0000 chunk 441 optimal weight: 10.0000 chunk 465 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN H 20 GLN L 66 ASN L 192 ASN L 200 ASN M 40 ASN N 32 ASN Q 7 HIS ** V 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 59 ASN V 68 ASN V 137 GLN ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.118 86434 Z= 0.665 Angle : 0.983 12.554 130233 Z= 0.479 Chirality : 0.055 0.347 16792 Planarity : 0.008 0.097 6241 Dihedral : 23.991 179.417 45376 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 5.16 % Allowed : 19.04 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.15), residues: 2500 helix: -1.12 (0.20), residues: 610 sheet: -1.69 (0.23), residues: 492 loop : -2.25 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP J 29 HIS 0.012 0.002 HIS E 102 PHE 0.026 0.003 PHE L 91 TYR 0.028 0.003 TYR V 141 ARG 0.009 0.001 ARG F 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 448 time to evaluate : 3.112 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8694 (ttmt) REVERT: A 112 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7737 (mm) REVERT: B 180 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: C 70 ARG cc_start: 0.7850 (mmt90) cc_final: 0.7617 (mmt-90) REVERT: E 66 THR cc_start: 0.8287 (p) cc_final: 0.7910 (m) REVERT: E 92 ARG cc_start: 0.7497 (mtm110) cc_final: 0.7108 (mtp-110) REVERT: G 60 GLU cc_start: 0.6892 (mp0) cc_final: 0.6627 (mm-30) REVERT: K 58 ARG cc_start: 0.7709 (tpt90) cc_final: 0.7428 (tpt170) REVERT: L 162 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7262 (ppt-90) REVERT: L 210 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: O 32 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7957 (mpp) REVERT: Q 52 LYS cc_start: 0.8081 (ptpt) cc_final: 0.7640 (mmtm) REVERT: S 158 ASN cc_start: 0.5617 (OUTLIER) cc_final: 0.5342 (t0) REVERT: W 87 ILE cc_start: 0.8686 (mm) cc_final: 0.8365 (pt) REVERT: Z 44 VAL cc_start: 0.9365 (p) cc_final: 0.9063 (t) outliers start: 111 outliers final: 96 residues processed: 515 average time/residue: 0.8454 time to fit residues: 721.5931 Evaluate side-chains 549 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 446 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 19 LYS Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 34 ARG Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 60 GLN Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 158 ASN Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain W residue 113 LYS Chi-restraints excluded: chain W residue 120 GLU Chi-restraints excluded: chain X residue 99 SER Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 119 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 92 ILE Chi-restraints excluded: chain a residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 306 optimal weight: 0.7980 chunk 493 optimal weight: 0.7980 chunk 301 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 343 optimal weight: 0.6980 chunk 518 optimal weight: 8.9990 chunk 476 optimal weight: 4.9990 chunk 412 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 318 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN H 85 GLN L 192 ASN O 4 ASN Q 7 HIS ** V 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 ASN V 68 ASN V 137 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 86434 Z= 0.148 Angle : 0.577 9.999 130233 Z= 0.300 Chirality : 0.035 0.293 16792 Planarity : 0.005 0.051 6241 Dihedral : 23.658 179.848 45376 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.11 % Allowed : 20.99 % Favored : 75.89 % 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: -2.12 (0.16), residues: 2500 helix: -0.38 (0.21), residues: 600 sheet: -1.45 (0.23), residues: 495 loop : -1.88 (0.15), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 48 HIS 0.005 0.001 HIS C 29 PHE 0.016 0.001 PHE S 139 TYR 0.025 0.001 TYR Y 74 ARG 0.006 0.000 ARG L 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 485 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8036 (ttmt) REVERT: A 112 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7749 (mm) REVERT: B 180 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: D 85 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8686 (ttpp) REVERT: E 66 THR cc_start: 0.8289 (p) cc_final: 0.7898 (m) REVERT: E 92 ARG cc_start: 0.7478 (mtm110) cc_final: 0.7033 (mtp-110) REVERT: H 19 LYS cc_start: 0.7503 (tmmt) cc_final: 0.6287 (mtpt) REVERT: I 35 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7296 (t0) REVERT: J 37 ARG cc_start: 0.7338 (ttm110) cc_final: 0.7097 (ttm110) REVERT: L 210 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: P 15 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8399 (mmtt) REVERT: Q 52 LYS cc_start: 0.7949 (ptpt) cc_final: 0.7541 (mmtm) REVERT: W 9 LYS cc_start: 0.7893 (mmmt) cc_final: 0.7481 (mmtt) REVERT: W 87 ILE cc_start: 0.8614 (mm) cc_final: 0.8269 (pt) REVERT: Y 57 TYR cc_start: 0.7878 (t80) cc_final: 0.7607 (t80) outliers start: 67 outliers final: 55 residues processed: 524 average time/residue: 0.8518 time to fit residues: 741.7154 Evaluate side-chains 538 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 478 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain W residue 113 LYS Chi-restraints excluded: chain X residue 99 SER Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 53 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 327 optimal weight: 6.9990 chunk 439 optimal weight: 7.9990 chunk 126 optimal weight: 0.3980 chunk 380 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 413 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 424 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 ASN O 22 ASN O 25 ASN S 182 ASN V 68 ASN V 137 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.145570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.129296 restraints weight = 110123.041| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 0.71 r_work: 0.3191 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 86434 Z= 0.219 Angle : 0.622 59.069 130233 Z= 0.331 Chirality : 0.037 0.732 16792 Planarity : 0.005 0.050 6241 Dihedral : 23.657 179.903 45376 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.92 % Rotamer: Outliers : 2.97 % Allowed : 21.32 % Favored : 75.71 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.16), residues: 2500 helix: -0.39 (0.21), residues: 604 sheet: -1.42 (0.23), residues: 495 loop : -1.86 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 48 HIS 0.006 0.001 HIS C 29 PHE 0.015 0.001 PHE S 139 TYR 0.023 0.002 TYR Y 74 ARG 0.008 0.000 ARG K 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13812.52 seconds wall clock time: 242 minutes 49.73 seconds (14569.73 seconds total)