Starting phenix.real_space_refine on Tue Jul 23 00:15:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/07_2024/6o7i_0642_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/07_2024/6o7i_0642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/07_2024/6o7i_0642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/07_2024/6o7i_0642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/07_2024/6o7i_0642_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/07_2024/6o7i_0642_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 48 5.49 5 S 60 5.16 5 C 12749 2.51 5 N 3555 2.21 5 O 3860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "A ARG 755": "NH1" <-> "NH2" Residue "A ARG 776": "NH1" <-> "NH2" Residue "A ARG 777": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "J ARG 74": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "K ARG 4": "NH1" <-> "NH2" Residue "K ARG 58": "NH1" <-> "NH2" Residue "K ARG 90": "NH1" <-> "NH2" Residue "K ARG 107": "NH1" <-> "NH2" Residue "K ARG 126": "NH1" <-> "NH2" Residue "K ARG 173": "NH1" <-> "NH2" Residue "K ARG 181": "NH1" <-> "NH2" Residue "K ARG 185": "NH1" <-> "NH2" Residue "K ARG 231": "NH1" <-> "NH2" Residue "K PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 4": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 383": "NH1" <-> "NH2" Residue "F ARG 384": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20276 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5935 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 6 Chain: "B" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1065 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 2191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2191 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2178 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain breaks: 2 Chain: "E" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2207 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 20, 'TRANS': 258} Chain breaks: 1 Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 907 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "G" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 569 Classifications: {'RNA': 26} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna2p': 12, 'rna3p': 13} Chain: "H" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 398 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "K" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2198 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 1 Chain: "I" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Chain: "F" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 313 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "F" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2223 Classifications: {'peptide': 322} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 106} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain breaks: 10 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 93, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 146 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3000 SG CYS A 389 61.945 108.426 107.521 1.00 26.96 S ATOM 3020 SG CYS A 392 57.962 106.580 107.991 1.00 25.58 S ATOM 3175 SG CYS A 413 59.672 108.840 110.942 1.00 33.04 S ATOM 3195 SG CYS A 416 60.786 105.552 110.270 1.00 32.70 S ATOM 7804 SG CYS C 113 78.649 118.893 83.547 1.00 26.80 S ATOM 7871 SG CYS C 122 80.218 118.407 80.144 1.00 17.37 S ATOM 7891 SG CYS C 125 76.481 116.361 82.122 1.00 21.96 S ATOM 10000 SG CYS D 113 95.191 89.112 86.916 1.00 29.12 S ATOM 10067 SG CYS D 122 97.096 88.689 83.714 1.00 23.66 S ATOM 10087 SG CYS D 125 93.080 88.859 83.641 1.00 23.54 S ATOM 16261 SG CYS K 113 95.575 55.229 83.185 1.00 56.33 S ATOM 16328 SG CYS K 122 98.462 54.545 81.147 1.00 52.56 S ATOM 16348 SG CYS K 125 94.722 56.298 79.316 1.00 44.05 S Time building chain proxies: 11.89, per 1000 atoms: 0.59 Number of scatterers: 20276 At special positions: 0 Unit cell: (129.591, 143.748, 168.795, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 60 16.00 P 48 15.00 O 3860 8.00 N 3555 7.00 C 12749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.19 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 413 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 392 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 416 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 125 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 111 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 111 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 122 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 125 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 111 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 122 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 125 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 113 " Number of angles added : 15 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4524 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 32 sheets defined 39.0% alpha, 14.9% beta 10 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 6.73 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 4.378A pdb=" N ALA A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 31 through 44 removed outlier: 5.210A pdb=" N PHE A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.793A pdb=" N LEU A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.823A pdb=" N ARG A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 106 removed outlier: 3.779A pdb=" N LEU A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.675A pdb=" N GLU A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 181 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.511A pdb=" N LEU A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 282 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 303 through 325 removed outlier: 3.715A pdb=" N LYS A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.564A pdb=" N HIS A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 removed outlier: 3.619A pdb=" N ASN A 417 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.951A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.874A pdb=" N PHE A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.653A pdb=" N THR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 559 removed outlier: 3.517A pdb=" N ILE A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 598 through 614 removed outlier: 3.848A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.996A pdb=" N VAL A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.772A pdb=" N ARG A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 713 removed outlier: 3.524A pdb=" N TRP A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 719 removed outlier: 3.934A pdb=" N VAL A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 713 through 719' Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.547A pdb=" N LEU A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 729 " --> pdb=" O TRP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 774 removed outlier: 4.421A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 4.373A pdb=" N TRP B 49 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 72 through 84 removed outlier: 3.736A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 removed outlier: 3.695A pdb=" N LEU B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 126 removed outlier: 4.056A pdb=" N ARG B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 removed outlier: 3.990A pdb=" N ARG B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 183 removed outlier: 3.863A pdb=" N GLN B 173 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 70 removed outlier: 3.595A pdb=" N LEU C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 removed outlier: 3.631A pdb=" N ALA C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 149 through 155 Processing helix chain 'C' and resid 205 through 220 removed outlier: 3.532A pdb=" N LEU C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.792A pdb=" N TYR C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.614A pdb=" N GLY C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 70 removed outlier: 4.052A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.714A pdb=" N GLU D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 223 Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'E' and resid 20 through 36 removed outlier: 3.728A pdb=" N ALA E 27 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 51 Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.895A pdb=" N VAL E 73 " --> pdb=" O PRO E 70 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU E 74 " --> pdb=" O LEU E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 74' Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.602A pdb=" N ILE E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 76 through 81' Processing helix chain 'E' and resid 90 through 99 removed outlier: 3.599A pdb=" N ALA E 99 " --> pdb=" O ARG E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 111 Processing helix chain 'E' and resid 164 through 171 removed outlier: 4.003A pdb=" N PHE E 168 " --> pdb=" O PRO E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'J' and resid 51 through 63 Processing helix chain 'J' and resid 72 through 83 removed outlier: 3.676A pdb=" N THR J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 100 Processing helix chain 'J' and resid 100 through 108 removed outlier: 3.822A pdb=" N THR J 104 " --> pdb=" O ASP J 100 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR J 105 " --> pdb=" O MET J 101 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU J 106 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU J 107 " --> pdb=" O ARG J 103 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS J 108 " --> pdb=" O THR J 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 100 through 108' Processing helix chain 'J' and resid 117 through 132 removed outlier: 4.311A pdb=" N VAL J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR J 130 " --> pdb=" O LEU J 126 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL J 131 " --> pdb=" O LEU J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 155 removed outlier: 4.257A pdb=" N VAL J 155 " --> pdb=" O PRO J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 178 removed outlier: 3.874A pdb=" N VAL J 176 " --> pdb=" O LEU J 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 62 removed outlier: 3.702A pdb=" N ARG K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 69 Processing helix chain 'K' and resid 115 through 120 Processing helix chain 'K' and resid 149 through 157 removed outlier: 4.197A pdb=" N LYS K 155 " --> pdb=" O GLU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 223 Processing helix chain 'K' and resid 249 through 254 Processing helix chain 'K' and resid 267 through 272 removed outlier: 3.572A pdb=" N ILE K 272 " --> pdb=" O SER K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 280 Processing helix chain 'K' and resid 280 through 287 Processing helix chain 'F' and resid 36 through 44 No H-bonds generated for 'chain 'F' and resid 36 through 44' Processing helix chain 'F' and resid 51 through 60 No H-bonds generated for 'chain 'F' and resid 51 through 60' Processing helix chain 'F' and resid 113 through 133 No H-bonds generated for 'chain 'F' and resid 113 through 133' Processing helix chain 'F' and resid 160 through 169 No H-bonds generated for 'chain 'F' and resid 160 through 169' Processing helix chain 'F' and resid 179 through 185 No H-bonds generated for 'chain 'F' and resid 179 through 185' Processing helix chain 'F' and resid 204 through 207 No H-bonds generated for 'chain 'F' and resid 204 through 207' Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 256 through 262 No H-bonds generated for 'chain 'F' and resid 256 through 262' Processing helix chain 'F' and resid 284 through 297 No H-bonds generated for 'chain 'F' and resid 284 through 297' Processing helix chain 'F' and resid 298 through 304 No H-bonds generated for 'chain 'F' and resid 298 through 304' Processing helix chain 'F' and resid 317 through 324 No H-bonds generated for 'chain 'F' and resid 317 through 324' Processing helix chain 'F' and resid 340 through 344 No H-bonds generated for 'chain 'F' and resid 340 through 344' Processing helix chain 'F' and resid 345 through 352 No H-bonds generated for 'chain 'F' and resid 345 through 352' Processing helix chain 'F' and resid 354 through 365 No H-bonds generated for 'chain 'F' and resid 354 through 365' Processing sheet with id=AA1, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.622A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N HIS A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.622A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N HIS A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AA4, first strand: chain 'A' and resid 402 through 403 Processing sheet with id=AA5, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.639A pdb=" N VAL A 444 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 580 through 585 removed outlier: 6.585A pdb=" N PHE A 591 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 594 " --> pdb=" O GLY A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AA8, first strand: chain 'C' and resid 49 through 50 removed outlier: 4.398A pdb=" N GLU C 195 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA C 146 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLU C 193 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU C 148 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLU C 191 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 190 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C 10 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE C 243 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS C 12 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 243 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 261 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 85 through 88 removed outlier: 7.316A pdb=" N SER C 85 " --> pdb=" O PHE C 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AB2, first strand: chain 'C' and resid 166 through 171 Processing sheet with id=AB3, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.702A pdb=" N PHE D 147 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.589A pdb=" N PHE D 194 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY D 13 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY D 7 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL D 10 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE D 243 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS D 12 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE D 243 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 85 through 88 removed outlier: 5.247A pdb=" N SER D 85 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE D 101 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLY D 87 " --> pdb=" O PHE D 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 103 through 104 Processing sheet with id=AB7, first strand: chain 'D' and resid 163 through 168 Processing sheet with id=AB8, first strand: chain 'E' and resid 58 through 61 removed outlier: 8.185A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL E 157 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 66 through 68 Processing sheet with id=AC1, first strand: chain 'E' and resid 124 through 132 Processing sheet with id=AC2, first strand: chain 'E' and resid 251 through 254 removed outlier: 4.022A pdb=" N SER E 251 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR E 211 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 229 through 232 Processing sheet with id=AC4, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC5, first strand: chain 'E' and resid 261 through 263 removed outlier: 3.806A pdb=" N VAL E 271 " --> pdb=" O LEU E 263 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 141 through 143 removed outlier: 3.963A pdb=" N GLY K 7 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE K 147 " --> pdb=" O GLU K 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 141 through 143 removed outlier: 3.963A pdb=" N GLY K 7 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL K 10 " --> pdb=" O PHE K 243 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE K 243 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS K 12 " --> pdb=" O ASP K 241 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP K 241 " --> pdb=" O LYS K 12 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE K 243 " --> pdb=" O SER K 261 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 85 through 88 removed outlier: 7.057A pdb=" N SER K 85 " --> pdb=" O PHE K 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'K' and resid 103 through 104 Processing sheet with id=AD1, first strand: chain 'K' and resid 163 through 168 removed outlier: 3.721A pdb=" N ARG K 181 " --> pdb=" O GLU K 168 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 248 through 251 WARNING: can't find one or more strands! previous: chain 'F' and resid 248 through 251 current: chain 'F' and resid 4 through 8 WARNING: can't find one or more strands! previous: chain 'F' and resid 4 through 8 current: chain 'F' and resid 393 through 396 WARNING: can't find one or more strands! previous: chain 'F' and resid 393 through 396 current: chain 'F' and resid 331 through 334 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 19 through 20 WARNING: can't find one or more strands! previous: chain 'F' and resid 19 through 20 current: chain 'F' and resid 100 through 101 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 209 through 211 WARNING: can't find one or more strands! previous: chain 'F' and resid 209 through 211 current: chain 'F' and resid 253 through 255 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'F' and resid 237 through 243 WARNING: can't find one or more strands! previous: chain 'F' and resid 237 through 243 current: chain 'F' and resid 222 through 230 WARNING: can't find one or more strands! previous: chain 'F' and resid 222 through 230 current: chain 'F' and resid 383 through 386 No H-bonds generated for sheet with id=AD5 581 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 6.23 Time building geometry restraints manager: 7.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4689 1.33 - 1.45: 4928 1.45 - 1.57: 10990 1.57 - 1.69: 93 1.69 - 1.82: 97 Bond restraints: 20797 Sorted by residual: bond pdb=" N ILE C 23 " pdb=" CA ILE C 23 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.82e+01 bond pdb=" CG LEU E 134 " pdb=" CD1 LEU E 134 " ideal model delta sigma weight residual 1.521 1.391 0.130 3.30e-02 9.18e+02 1.56e+01 bond pdb=" CG1 ILE D 40 " pdb=" CD1 ILE D 40 " ideal model delta sigma weight residual 1.513 1.378 0.135 3.90e-02 6.57e+02 1.20e+01 bond pdb=" CB PRO C 51 " pdb=" CG PRO C 51 " ideal model delta sigma weight residual 1.492 1.323 0.169 5.00e-02 4.00e+02 1.15e+01 bond pdb=" CB ILE E 143 " pdb=" CG2 ILE E 143 " ideal model delta sigma weight residual 1.521 1.411 0.110 3.30e-02 9.18e+02 1.12e+01 ... (remaining 20792 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.41: 658 105.41 - 112.60: 10221 112.60 - 119.79: 7711 119.79 - 126.97: 9363 126.97 - 134.16: 360 Bond angle restraints: 28313 Sorted by residual: angle pdb=" C4' C G 14 " pdb=" C3' C G 14 " pdb=" O3' C G 14 " ideal model delta sigma weight residual 109.40 100.83 8.57 1.50e+00 4.44e-01 3.26e+01 angle pdb=" N ASP D 2 " pdb=" CA ASP D 2 " pdb=" C ASP D 2 " ideal model delta sigma weight residual 110.91 117.26 -6.35 1.17e+00 7.31e-01 2.94e+01 angle pdb=" C4' G G 9 " pdb=" C3' G G 9 " pdb=" O3' G G 9 " ideal model delta sigma weight residual 109.40 101.48 7.92 1.50e+00 4.44e-01 2.78e+01 angle pdb=" N VAL A 753 " pdb=" CA VAL A 753 " pdb=" C VAL A 753 " ideal model delta sigma weight residual 112.29 107.40 4.89 9.40e-01 1.13e+00 2.70e+01 angle pdb=" C GLY A 376 " pdb=" N LEU A 377 " pdb=" CA LEU A 377 " ideal model delta sigma weight residual 120.28 127.24 -6.96 1.34e+00 5.57e-01 2.70e+01 ... (remaining 28308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.33: 12197 33.33 - 66.65: 258 66.65 - 99.98: 28 99.98 - 133.31: 0 133.31 - 166.64: 1 Dihedral angle restraints: 12484 sinusoidal: 5429 harmonic: 7055 Sorted by residual: dihedral pdb=" O4' C G 14 " pdb=" C1' C G 14 " pdb=" N1 C G 14 " pdb=" C2 C G 14 " ideal model delta sinusoidal sigma weight residual -128.00 38.64 -166.64 1 1.70e+01 3.46e-03 6.55e+01 dihedral pdb=" O4' U H 29 " pdb=" C1' U H 29 " pdb=" N1 U H 29 " pdb=" C2 U H 29 " ideal model delta sinusoidal sigma weight residual -160.00 -79.30 -80.70 1 1.50e+01 4.44e-03 3.58e+01 dihedral pdb=" CA LYS A 369 " pdb=" C LYS A 369 " pdb=" N ARG A 370 " pdb=" CA ARG A 370 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 12481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2350 0.073 - 0.147: 624 0.147 - 0.220: 116 0.220 - 0.293: 24 0.293 - 0.367: 7 Chirality restraints: 3121 Sorted by residual: chirality pdb=" CB VAL E 157 " pdb=" CA VAL E 157 " pdb=" CG1 VAL E 157 " pdb=" CG2 VAL E 157 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB VAL E 132 " pdb=" CA VAL E 132 " pdb=" CG1 VAL E 132 " pdb=" CG2 VAL E 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB VAL C 236 " pdb=" CA VAL C 236 " pdb=" CG1 VAL C 236 " pdb=" CG2 VAL C 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 3118 not shown) Planarity restraints: 3462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G G 13 " -0.048 2.00e-02 2.50e+03 2.01e-02 1.21e+01 pdb=" N9 G G 13 " 0.045 2.00e-02 2.50e+03 pdb=" C8 G G 13 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G G 13 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G G 13 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G G 13 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G G 13 " -0.019 2.00e-02 2.50e+03 pdb=" N1 G G 13 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G G 13 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G G 13 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G G 13 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G G 13 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 389 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO A 390 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 390 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 390 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 13 " -0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO E 14 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " -0.045 5.00e-02 4.00e+02 ... (remaining 3459 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 3561 2.76 - 3.47: 26157 3.47 - 4.19: 48781 4.19 - 4.90: 86066 Nonbonded interactions: 164566 Sorted by model distance: nonbonded pdb=" C ARG F 39 " pdb=" N UNK F 40 " model vdw 1.331 3.350 nonbonded pdb=" O2' G G 9 " pdb=" C5 C G 10 " model vdw 2.131 3.340 nonbonded pdb=" O2' C G 10 " pdb=" O5' G G 11 " model vdw 2.203 2.440 nonbonded pdb=" O THR A 435 " pdb=" OG SER A 449 " model vdw 2.244 2.440 nonbonded pdb=" OE2 GLU C 168 " pdb=" OH TYR C 233 " model vdw 2.244 2.440 ... (remaining 164561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 4 through 24 or resid 38 through 272 or resid 276 through \ 287 or resid 301)) selection = (chain 'D' and (resid 4 through 24 or resid 38 through 287 or resid 301)) selection = (chain 'K' and (resid 4 through 24 or resid 38 through 272 or resid 276 through \ 287 or resid 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.080 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 60.320 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.169 20797 Z= 0.761 Angle : 1.170 10.493 28313 Z= 0.649 Chirality : 0.070 0.367 3121 Planarity : 0.008 0.087 3462 Dihedral : 13.656 166.637 7960 Min Nonbonded Distance : 1.331 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.17 % Favored : 91.78 % Rotamer: Outliers : 1.03 % Allowed : 5.28 % Favored : 93.69 % 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: -4.51 (0.14), residues: 2325 helix: -3.32 (0.12), residues: 803 sheet: -2.61 (0.24), residues: 348 loop : -2.84 (0.15), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP A 131 HIS 0.015 0.003 HIS A 14 PHE 0.043 0.005 PHE A 502 TYR 0.044 0.004 TYR A 265 ARG 0.022 0.002 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 422 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.8136 (m-80) cc_final: 0.7922 (m-10) REVERT: A 159 LYS cc_start: 0.8263 (tmmt) cc_final: 0.7932 (mmmm) REVERT: A 493 LYS cc_start: 0.7926 (ptpp) cc_final: 0.7669 (mtmm) REVERT: A 600 PHE cc_start: 0.7788 (t80) cc_final: 0.7467 (t80) REVERT: A 711 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6807 (mm-30) REVERT: B 152 MET cc_start: 0.6926 (mtm) cc_final: 0.5856 (mmt) REVERT: E 38 GLN cc_start: 0.8060 (tt0) cc_final: 0.7858 (tt0) REVERT: E 128 ASP cc_start: 0.8060 (p0) cc_final: 0.7697 (p0) REVERT: J 101 MET cc_start: 0.3046 (tpt) cc_final: 0.2532 (tpt) REVERT: K 181 ARG cc_start: 0.7003 (pmt170) cc_final: 0.4807 (pmt170) REVERT: F 262 LEU cc_start: 0.7431 (mt) cc_final: 0.6450 (tp) REVERT: F 283 GLU cc_start: 0.4352 (tm-30) cc_final: 0.4145 (mm-30) REVERT: F 344 MET cc_start: 0.4155 (mmm) cc_final: 0.2337 (tmm) REVERT: F 391 MET cc_start: -0.0444 (ptm) cc_final: -0.1081 (ptm) outliers start: 20 outliers final: 7 residues processed: 434 average time/residue: 0.4045 time to fit residues: 248.1884 Evaluate side-chains 287 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 280 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 132 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 167 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 382 HIS B 72 ASN C 179 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS D 106 ASN E 200 HIS J 173 GLN K 22 HIS K 179 ASN F 18 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20797 Z= 0.189 Angle : 0.592 8.720 28313 Z= 0.304 Chirality : 0.043 0.188 3121 Planarity : 0.005 0.060 3462 Dihedral : 14.183 168.778 3472 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.26 % Allowed : 9.24 % Favored : 88.51 % 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: -3.37 (0.15), residues: 2325 helix: -1.95 (0.15), residues: 864 sheet: -2.10 (0.26), residues: 327 loop : -2.47 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 131 HIS 0.007 0.001 HIS A 60 PHE 0.025 0.001 PHE A 561 TYR 0.015 0.001 TYR B 140 ARG 0.006 0.001 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 329 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ARG cc_start: 0.7034 (ttp-110) cc_final: 0.6828 (ttm110) REVERT: A 156 GLU cc_start: 0.6623 (tp30) cc_final: 0.6288 (tp30) REVERT: A 161 LEU cc_start: 0.8688 (tp) cc_final: 0.8284 (tp) REVERT: A 501 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7494 (p) REVERT: A 532 MET cc_start: 0.8572 (mpp) cc_final: 0.8170 (mpp) REVERT: A 533 ASP cc_start: 0.8141 (p0) cc_final: 0.7860 (p0) REVERT: A 600 PHE cc_start: 0.7546 (t80) cc_final: 0.7239 (t80) REVERT: B 152 MET cc_start: 0.6634 (mtm) cc_final: 0.5733 (mmt) REVERT: D 90 ARG cc_start: 0.7568 (ttm-80) cc_final: 0.7289 (ttp-170) REVERT: D 115 ASP cc_start: 0.7611 (m-30) cc_final: 0.7397 (m-30) REVERT: E 22 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.7006 (m-30) REVERT: J 101 MET cc_start: 0.3025 (tpt) cc_final: 0.2566 (tpt) REVERT: F 132 GLU cc_start: 0.3335 (tm-30) cc_final: 0.2928 (mt-10) REVERT: F 262 LEU cc_start: 0.7060 (mt) cc_final: 0.6291 (tp) REVERT: F 284 VAL cc_start: 0.3285 (OUTLIER) cc_final: 0.3068 (p) REVERT: F 344 MET cc_start: 0.3980 (mmm) cc_final: 0.1579 (tmm) REVERT: F 391 MET cc_start: -0.0843 (ptm) cc_final: -0.1385 (ptm) outliers start: 44 outliers final: 19 residues processed: 355 average time/residue: 0.3756 time to fit residues: 193.3433 Evaluate side-chains 286 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 264 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 284 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 173 optimal weight: 0.0970 chunk 193 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 HIS ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20797 Z= 0.167 Angle : 0.545 10.054 28313 Z= 0.277 Chirality : 0.042 0.184 3121 Planarity : 0.005 0.053 3462 Dihedral : 13.935 167.882 3466 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.57 % Allowed : 11.19 % Favored : 86.25 % 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: -2.68 (0.16), residues: 2325 helix: -1.21 (0.17), residues: 872 sheet: -1.86 (0.26), residues: 326 loop : -2.19 (0.16), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 271 HIS 0.007 0.001 HIS A 60 PHE 0.017 0.001 PHE C 276 TYR 0.019 0.001 TYR K 224 ARG 0.007 0.000 ARG K 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 287 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7810 (pp20) cc_final: 0.7515 (tm-30) REVERT: A 501 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7472 (p) REVERT: A 545 MET cc_start: 0.8335 (tpp) cc_final: 0.8128 (tpp) REVERT: A 600 PHE cc_start: 0.7578 (t80) cc_final: 0.7293 (t80) REVERT: B 152 MET cc_start: 0.6641 (mtm) cc_final: 0.5705 (mmt) REVERT: C 107 ARG cc_start: 0.8314 (ttp80) cc_final: 0.7968 (ttp80) REVERT: C 233 TYR cc_start: 0.8184 (m-10) cc_final: 0.7943 (m-10) REVERT: C 276 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6621 (m-80) REVERT: D 64 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7790 (mm-30) REVERT: D 90 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.7275 (ttp-170) REVERT: E 203 LYS cc_start: 0.7752 (ttpp) cc_final: 0.7426 (ttpp) REVERT: J 101 MET cc_start: 0.3011 (tpt) cc_final: 0.2585 (tpt) REVERT: K 66 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8253 (tt) REVERT: K 153 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: K 187 VAL cc_start: 0.8211 (p) cc_final: 0.7993 (m) REVERT: F 344 MET cc_start: 0.3983 (mmm) cc_final: 0.1558 (tmm) REVERT: F 391 MET cc_start: -0.0802 (ptm) cc_final: -0.1358 (ptm) outliers start: 50 outliers final: 26 residues processed: 317 average time/residue: 0.3680 time to fit residues: 171.3462 Evaluate side-chains 279 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 249 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 153 GLU Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 211 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 55 optimal weight: 0.0670 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20797 Z= 0.169 Angle : 0.532 12.209 28313 Z= 0.268 Chirality : 0.042 0.238 3121 Planarity : 0.004 0.050 3462 Dihedral : 13.782 167.846 3466 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.92 % Allowed : 12.01 % Favored : 85.07 % 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: -2.23 (0.16), residues: 2325 helix: -0.75 (0.17), residues: 878 sheet: -1.61 (0.27), residues: 330 loop : -2.01 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 152 HIS 0.006 0.001 HIS A 60 PHE 0.017 0.001 PHE C 276 TYR 0.017 0.001 TYR K 224 ARG 0.006 0.000 ARG D 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 269 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7584 (mtm-85) cc_final: 0.7267 (mtm180) REVERT: A 501 THR cc_start: 0.7841 (OUTLIER) cc_final: 0.7436 (p) REVERT: A 545 MET cc_start: 0.8374 (tpp) cc_final: 0.8161 (tpp) REVERT: A 558 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6874 (tm-30) REVERT: A 600 PHE cc_start: 0.7642 (t80) cc_final: 0.7352 (t80) REVERT: B 123 MET cc_start: 0.4264 (OUTLIER) cc_final: 0.3938 (ttt) REVERT: B 152 MET cc_start: 0.6600 (mtm) cc_final: 0.5692 (mmt) REVERT: C 276 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: D 64 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7652 (mm-30) REVERT: D 92 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6805 (p0) REVERT: E 22 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7062 (m-30) REVERT: E 203 LYS cc_start: 0.7783 (ttpp) cc_final: 0.7561 (ttpp) REVERT: J 101 MET cc_start: 0.2940 (tpt) cc_final: 0.2477 (tpt) REVERT: F 344 MET cc_start: 0.4056 (mmm) cc_final: 0.1581 (tmm) REVERT: F 391 MET cc_start: -0.0809 (ptm) cc_final: -0.1357 (ptm) outliers start: 57 outliers final: 33 residues processed: 303 average time/residue: 0.3348 time to fit residues: 152.5035 Evaluate side-chains 292 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 254 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 212 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 30.0000 chunk 117 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 176 optimal weight: 0.0010 chunk 142 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20797 Z= 0.269 Angle : 0.582 11.885 28313 Z= 0.294 Chirality : 0.044 0.280 3121 Planarity : 0.004 0.052 3462 Dihedral : 13.782 160.756 3466 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.08 % Allowed : 12.93 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.17), residues: 2325 helix: -0.60 (0.17), residues: 888 sheet: -1.47 (0.27), residues: 335 loop : -1.96 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 156 HIS 0.006 0.001 HIS A 60 PHE 0.023 0.001 PHE C 276 TYR 0.017 0.002 TYR K 224 ARG 0.005 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 256 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7097 (mtp-110) cc_final: 0.6675 (ttm110) REVERT: A 545 MET cc_start: 0.8458 (tpp) cc_final: 0.8219 (tpt) REVERT: A 558 GLU cc_start: 0.7232 (tm-30) cc_final: 0.7005 (tm-30) REVERT: A 600 PHE cc_start: 0.7799 (t80) cc_final: 0.7474 (t80) REVERT: B 123 MET cc_start: 0.4446 (OUTLIER) cc_final: 0.4148 (ttt) REVERT: B 152 MET cc_start: 0.6634 (mtm) cc_final: 0.5715 (mmt) REVERT: C 276 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6843 (m-80) REVERT: D 92 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6909 (p0) REVERT: D 184 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: E 22 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7053 (m-30) REVERT: J 101 MET cc_start: 0.2935 (tpt) cc_final: 0.2472 (tpt) REVERT: F 344 MET cc_start: 0.4195 (mmm) cc_final: 0.2127 (tmm) outliers start: 60 outliers final: 40 residues processed: 296 average time/residue: 0.3636 time to fit residues: 159.0685 Evaluate side-chains 286 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 241 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 258 ASP Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 212 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 121 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 171 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN C 183 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN E 139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20797 Z= 0.154 Angle : 0.524 12.719 28313 Z= 0.262 Chirality : 0.041 0.206 3121 Planarity : 0.004 0.047 3462 Dihedral : 13.714 165.105 3466 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.57 % Allowed : 13.75 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.17), residues: 2325 helix: -0.25 (0.18), residues: 892 sheet: -1.22 (0.28), residues: 307 loop : -1.79 (0.17), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 156 HIS 0.004 0.001 HIS A 60 PHE 0.026 0.001 PHE A 561 TYR 0.013 0.001 TYR K 224 ARG 0.005 0.000 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 256 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 545 MET cc_start: 0.8437 (tpp) cc_final: 0.8089 (tpp) REVERT: A 600 PHE cc_start: 0.7739 (t80) cc_final: 0.7366 (t80) REVERT: A 692 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7648 (t0) REVERT: B 123 MET cc_start: 0.4503 (OUTLIER) cc_final: 0.4066 (ttt) REVERT: B 152 MET cc_start: 0.6575 (mtm) cc_final: 0.5691 (mmt) REVERT: C 276 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6825 (m-80) REVERT: D 64 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7815 (mm-30) REVERT: D 92 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6978 (p0) REVERT: D 184 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7153 (tt0) REVERT: E 128 ASP cc_start: 0.7730 (p0) cc_final: 0.7309 (p0) REVERT: J 101 MET cc_start: 0.2800 (tpt) cc_final: 0.2564 (tpt) REVERT: F 3 GLU cc_start: 0.4888 (tm-30) cc_final: 0.3851 (mm-30) REVERT: F 289 LEU cc_start: 0.7091 (tt) cc_final: 0.6396 (mt) REVERT: F 344 MET cc_start: 0.4125 (mmm) cc_final: 0.1512 (tmm) outliers start: 50 outliers final: 34 residues processed: 287 average time/residue: 0.3505 time to fit residues: 149.8995 Evaluate side-chains 278 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 239 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 6 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 9.9990 chunk 23 optimal weight: 0.0020 chunk 117 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 174 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 127 optimal weight: 0.3980 overall best weight: 1.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20797 Z= 0.218 Angle : 0.552 13.332 28313 Z= 0.277 Chirality : 0.043 0.198 3121 Planarity : 0.004 0.048 3462 Dihedral : 13.705 163.343 3466 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.03 % Allowed : 13.39 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.17), residues: 2325 helix: -0.15 (0.18), residues: 892 sheet: -1.13 (0.27), residues: 326 loop : -1.78 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 156 HIS 0.006 0.001 HIS C 205 PHE 0.046 0.001 PHE A 561 TYR 0.014 0.001 TYR F 111 ARG 0.005 0.000 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 246 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 545 MET cc_start: 0.8547 (tpp) cc_final: 0.8256 (tpt) REVERT: A 600 PHE cc_start: 0.7775 (t80) cc_final: 0.7425 (t80) REVERT: A 692 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7670 (t0) REVERT: B 123 MET cc_start: 0.4459 (OUTLIER) cc_final: 0.4232 (ttt) REVERT: B 152 MET cc_start: 0.6594 (mtm) cc_final: 0.5697 (mmt) REVERT: C 276 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6979 (m-80) REVERT: D 92 ASP cc_start: 0.7128 (OUTLIER) cc_final: 0.6894 (p0) REVERT: D 184 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: E 22 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.7000 (m-30) REVERT: K 267 LYS cc_start: 0.7522 (mmmt) cc_final: 0.7066 (tttt) REVERT: F 3 GLU cc_start: 0.4670 (tm-30) cc_final: 0.3810 (mm-30) REVERT: F 289 LEU cc_start: 0.7231 (tt) cc_final: 0.6530 (mt) REVERT: F 344 MET cc_start: 0.4334 (mmm) cc_final: 0.1765 (tmm) REVERT: F 397 GLU cc_start: 0.4996 (pp20) cc_final: 0.3072 (tt0) outliers start: 59 outliers final: 41 residues processed: 286 average time/residue: 0.3496 time to fit residues: 148.4041 Evaluate side-chains 286 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 239 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 149 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 187 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20797 Z= 0.152 Angle : 0.517 13.594 28313 Z= 0.259 Chirality : 0.041 0.204 3121 Planarity : 0.004 0.047 3462 Dihedral : 13.665 166.889 3466 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.26 % Allowed : 14.47 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2325 helix: 0.07 (0.18), residues: 890 sheet: -1.00 (0.29), residues: 307 loop : -1.70 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 156 HIS 0.005 0.001 HIS C 205 PHE 0.042 0.001 PHE A 561 TYR 0.015 0.001 TYR F 111 ARG 0.006 0.000 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 240 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 MET cc_start: 0.8503 (tpp) cc_final: 0.8184 (tpt) REVERT: A 600 PHE cc_start: 0.7716 (t80) cc_final: 0.7370 (t80) REVERT: A 692 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7660 (t0) REVERT: B 152 MET cc_start: 0.6318 (mtm) cc_final: 0.5517 (mmt) REVERT: B 153 LEU cc_start: 0.5413 (mm) cc_final: 0.4536 (tp) REVERT: C 276 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.6922 (m-80) REVERT: D 184 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: E 22 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: E 128 ASP cc_start: 0.7769 (p0) cc_final: 0.7327 (p0) REVERT: J 101 MET cc_start: 0.2666 (tpt) cc_final: 0.2455 (tpt) REVERT: K 183 ASN cc_start: 0.6837 (t0) cc_final: 0.6584 (t0) REVERT: K 267 LYS cc_start: 0.7436 (mmmt) cc_final: 0.6940 (tttt) REVERT: F 3 GLU cc_start: 0.4518 (tm-30) cc_final: 0.3729 (mm-30) REVERT: F 344 MET cc_start: 0.4401 (mmm) cc_final: 0.1641 (tmm) REVERT: F 397 GLU cc_start: 0.5050 (pp20) cc_final: 0.3255 (tt0) outliers start: 44 outliers final: 30 residues processed: 271 average time/residue: 0.3419 time to fit residues: 140.5516 Evaluate side-chains 255 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 221 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain F residue 6 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.8980 chunk 180 optimal weight: 7.9990 chunk 192 optimal weight: 0.3980 chunk 115 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 173 optimal weight: 0.2980 chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20797 Z= 0.149 Angle : 0.517 13.328 28313 Z= 0.258 Chirality : 0.041 0.245 3121 Planarity : 0.004 0.047 3462 Dihedral : 13.616 169.269 3466 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.05 % Allowed : 14.47 % Favored : 83.48 % 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: -1.24 (0.17), residues: 2325 helix: 0.18 (0.18), residues: 900 sheet: -0.99 (0.29), residues: 305 loop : -1.61 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 156 HIS 0.005 0.001 HIS A 60 PHE 0.036 0.001 PHE A 561 TYR 0.016 0.001 TYR K 250 ARG 0.006 0.000 ARG K 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 235 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.6864 (ttp80) cc_final: 0.6558 (ttp80) REVERT: A 545 MET cc_start: 0.8507 (tpp) cc_final: 0.8208 (tpt) REVERT: A 600 PHE cc_start: 0.7703 (t80) cc_final: 0.7351 (t80) REVERT: A 692 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7664 (t0) REVERT: B 152 MET cc_start: 0.6366 (mtm) cc_final: 0.5533 (mmt) REVERT: B 153 LEU cc_start: 0.5332 (mm) cc_final: 0.4460 (tp) REVERT: C 276 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6968 (m-80) REVERT: D 184 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: E 22 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.7055 (m-30) REVERT: J 101 MET cc_start: 0.2639 (tpt) cc_final: 0.2192 (tpt) REVERT: K 183 ASN cc_start: 0.6813 (t0) cc_final: 0.6535 (t0) REVERT: K 267 LYS cc_start: 0.7473 (mmmt) cc_final: 0.6983 (tttt) REVERT: F 3 GLU cc_start: 0.4289 (tm-30) cc_final: 0.3583 (mm-30) REVERT: F 397 GLU cc_start: 0.5052 (pp20) cc_final: 0.3285 (tt0) outliers start: 40 outliers final: 30 residues processed: 265 average time/residue: 0.3551 time to fit residues: 140.5931 Evaluate side-chains 263 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 229 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 213 optimal weight: 50.0000 chunk 196 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 131 optimal weight: 0.0370 chunk 104 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 205 HIS ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20797 Z= 0.160 Angle : 0.531 13.702 28313 Z= 0.265 Chirality : 0.042 0.200 3121 Planarity : 0.004 0.047 3462 Dihedral : 13.585 169.314 3466 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.90 % Allowed : 14.93 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.17), residues: 2325 helix: 0.22 (0.18), residues: 900 sheet: -0.87 (0.29), residues: 307 loop : -1.59 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 156 HIS 0.005 0.001 HIS A 60 PHE 0.039 0.001 PHE A 561 TYR 0.018 0.001 TYR K 224 ARG 0.006 0.000 ARG C 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 234 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.6826 (ttp80) cc_final: 0.6519 (ttp80) REVERT: A 545 MET cc_start: 0.8516 (tpp) cc_final: 0.8221 (tpt) REVERT: A 600 PHE cc_start: 0.7680 (t80) cc_final: 0.7338 (t80) REVERT: A 692 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7664 (t0) REVERT: B 152 MET cc_start: 0.6383 (mtm) cc_final: 0.5410 (mmt) REVERT: B 153 LEU cc_start: 0.5235 (mm) cc_final: 0.4411 (tp) REVERT: C 276 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.6966 (m-80) REVERT: E 22 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.7066 (m-30) REVERT: K 183 ASN cc_start: 0.6825 (t0) cc_final: 0.6581 (t0) REVERT: K 267 LYS cc_start: 0.7485 (mmmt) cc_final: 0.6993 (tttt) REVERT: F 3 GLU cc_start: 0.4321 (tm-30) cc_final: 0.3661 (mm-30) REVERT: F 397 GLU cc_start: 0.4894 (pp20) cc_final: 0.3308 (tt0) outliers start: 37 outliers final: 28 residues processed: 259 average time/residue: 0.3554 time to fit residues: 137.8093 Evaluate side-chains 256 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 225 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 0.0870 chunk 170 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.202946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.157578 restraints weight = 25381.917| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.39 r_work: 0.3229 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20797 Z= 0.137 Angle : 0.530 18.688 28313 Z= 0.260 Chirality : 0.041 0.175 3121 Planarity : 0.004 0.048 3462 Dihedral : 13.540 171.794 3466 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.49 % Allowed : 15.50 % Favored : 83.02 % 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: -0.97 (0.17), residues: 2325 helix: 0.40 (0.18), residues: 897 sheet: -0.63 (0.31), residues: 286 loop : -1.50 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 109 HIS 0.004 0.001 HIS A 60 PHE 0.036 0.001 PHE A 561 TYR 0.017 0.001 TYR K 224 ARG 0.005 0.000 ARG A 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4369.11 seconds wall clock time: 78 minutes 21.53 seconds (4701.53 seconds total)