Starting phenix.real_space_refine on Sun Feb 18 00:28:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/02_2024/6o7i_0642_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/02_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_0642/02_2024/6o7i_0642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/02_2024/6o7i_0642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/02_2024/6o7i_0642_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/02_2024/6o7i_0642_neut.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20276 Number of models: 1 Model: "" Number of chains: 15 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: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2536 Classifications: {'peptide': 361} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 106} Link IDs: {'PTRANS': 15, 'TRANS': 345} 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: 10.90, per 1000 atoms: 0.54 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: 8.27 Conformation dependent library (CDL) restraints added in 3.5 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: 6.66 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 removed outlier: 4.420A pdb=" N UNK F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 60 removed outlier: 3.572A pdb=" N UNK F 55 " --> pdb=" O UNK F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 133 removed outlier: 3.785A pdb=" N LEU F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 169 removed outlier: 3.716A pdb=" N UNK F 166 " --> pdb=" O UNK F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 185 removed outlier: 3.785A pdb=" N UNK F 183 " --> pdb=" O UNK F 179 " (cutoff:3.500A) Processing helix 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 removed outlier: 3.505A pdb=" N LEU F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG F 261 " --> pdb=" O THR F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.654A pdb=" N ALA F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR F 297 " --> pdb=" O VAL F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 304 Processing helix chain 'F' and resid 317 through 324 Processing helix chain 'F' and resid 340 through 344 removed outlier: 3.666A pdb=" N ALA F 343 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET F 344 " --> pdb=" O TRP F 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 340 through 344' Processing helix chain 'F' and resid 345 through 352 removed outlier: 4.099A pdb=" N LEU F 348 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL F 351 " --> pdb=" O LEU F 348 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU F 352 " --> pdb=" O LEU F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 365 removed outlier: 4.025A pdb=" N VAL F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS F 363 " --> pdb=" O ASN F 359 " (cutoff:3.500A) 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 Processing sheet with id=AD3, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.668A pdb=" N ILE F 100 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 209 through 211 Processing sheet with id=AD5, first strand: chain 'F' and resid 237 through 243 removed outlier: 3.723A pdb=" N LEU F 385 " --> pdb=" O GLU F 228 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1902 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: 6.96 Time building geometry restraints manager: 8.80 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: 4929 1.45 - 1.57: 10990 1.57 - 1.69: 93 1.69 - 1.82: 97 Bond restraints: 20798 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 20793 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.41: 658 105.41 - 112.60: 10221 112.60 - 119.79: 7712 119.79 - 126.97: 9365 126.97 - 134.16: 360 Bond angle restraints: 28316 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 28311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.33: 12198 33.33 - 66.65: 258 66.65 - 99.98: 28 99.98 - 133.31: 0 133.31 - 166.64: 1 Dihedral angle restraints: 12485 sinusoidal: 5429 harmonic: 7056 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 12482 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: 3463 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 3460 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 700 2.68 - 3.24: 18183 3.24 - 3.79: 31834 3.79 - 4.35: 42391 4.35 - 4.90: 71150 Nonbonded interactions: 164258 Sorted by model distance: 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 nonbonded pdb=" O ARG B 124 " pdb=" OH TYR J 178 " model vdw 2.251 2.440 ... (remaining 164253 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: 2.030 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: 0.010 Extract box with map and model: 4.710 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 62.470 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.100 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.340 ------------------------------------------------------------------------------- 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 20798 Z= 0.761 Angle : 1.170 10.493 28316 Z= 0.649 Chirality : 0.070 0.367 3121 Planarity : 0.008 0.087 3463 Dihedral : 13.655 166.637 7961 Min Nonbonded Distance : 2.131 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: -4.50 (0.14), residues: 2325 helix: -3.32 (0.12), residues: 803 sheet: -2.58 (0.24), residues: 359 loop : -2.84 (0.15), residues: 1163 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 : 2.204 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: 0.4138 time to fit residues: 252.5483 Evaluate side-chains 287 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 280 time to evaluate : 2.259 ------------------------------------------------------------------------------- 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: 211 random chunks: chunk 178 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 0.0470 chunk 54 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- 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: 0.7423 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20798 Z= 0.181 Angle : 0.596 8.958 28316 Z= 0.306 Chirality : 0.043 0.189 3121 Planarity : 0.005 0.060 3463 Dihedral : 14.193 170.050 3473 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.00 % Allowed : 9.29 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.15), residues: 2325 helix: -1.89 (0.15), residues: 861 sheet: -2.05 (0.26), residues: 331 loop : -2.45 (0.16), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 131 HIS 0.006 0.001 HIS A 60 PHE 0.027 0.001 PHE A 561 TYR 0.014 0.001 TYR B 140 ARG 0.005 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 370 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 331 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ARG cc_start: 0.7038 (ttp-110) cc_final: 0.6829 (ttm110) REVERT: A 156 GLU cc_start: 0.6654 (tp30) cc_final: 0.6292 (tp30) REVERT: A 161 LEU cc_start: 0.8679 (tp) cc_final: 0.8262 (tp) REVERT: A 501 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7453 (p) REVERT: A 524 ARG cc_start: 0.7325 (mtp180) cc_final: 0.7053 (mmm160) REVERT: A 532 MET cc_start: 0.8576 (mpp) cc_final: 0.8158 (mpp) REVERT: A 533 ASP cc_start: 0.8146 (p0) cc_final: 0.7805 (p0) REVERT: A 600 PHE cc_start: 0.7564 (t80) cc_final: 0.7282 (t80) REVERT: B 152 MET cc_start: 0.6732 (mtm) cc_final: 0.5757 (mmt) REVERT: D 90 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.7291 (ttp-170) REVERT: D 115 ASP cc_start: 0.7602 (m-30) cc_final: 0.7365 (m-30) REVERT: F 3 GLU cc_start: 0.4331 (tm-30) cc_final: 0.3766 (mp0) REVERT: F 258 GLU cc_start: 0.4667 (tp30) cc_final: 0.3779 (mm-30) REVERT: F 262 LEU cc_start: 0.6999 (mt) cc_final: 0.5775 (tp) REVERT: F 284 VAL cc_start: 0.3312 (OUTLIER) cc_final: 0.2977 (p) REVERT: F 301 MET cc_start: 0.0080 (ttm) cc_final: -0.1490 (ttm) REVERT: F 344 MET cc_start: 0.4077 (mmm) cc_final: 0.1497 (tmm) REVERT: F 391 MET cc_start: -0.0858 (ptm) cc_final: -0.1396 (ptm) outliers start: 39 outliers final: 18 residues processed: 355 average time/residue: 0.3823 time to fit residues: 196.1823 Evaluate side-chains 281 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 261 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU 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 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 66 LEU 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 284 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 170 optimal weight: 30.0000 chunk 190 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 HIS C 136 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20798 Z= 0.242 Angle : 0.597 10.235 28316 Z= 0.302 Chirality : 0.044 0.212 3121 Planarity : 0.005 0.056 3463 Dihedral : 13.974 161.598 3467 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.77 % Allowed : 11.65 % Favored : 85.58 % 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: -2.67 (0.16), residues: 2325 helix: -1.14 (0.17), residues: 867 sheet: -1.91 (0.25), residues: 349 loop : -2.19 (0.17), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 271 HIS 0.008 0.001 HIS A 60 PHE 0.023 0.001 PHE C 276 TYR 0.018 0.001 TYR K 224 ARG 0.007 0.001 ARG D 181 *********************** 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 330 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 276 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7817 (pp20) cc_final: 0.7529 (tm-30) REVERT: A 501 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7414 (p) REVERT: A 545 MET cc_start: 0.8339 (tpp) cc_final: 0.8054 (tpt) REVERT: A 558 GLU cc_start: 0.7213 (tm-30) cc_final: 0.7004 (tm-30) REVERT: A 600 PHE cc_start: 0.7639 (t80) cc_final: 0.7333 (t80) REVERT: B 152 MET cc_start: 0.6719 (mtm) cc_final: 0.5734 (mmt) REVERT: C 276 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: D 90 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7349 (ttp-170) REVERT: D 115 ASP cc_start: 0.8030 (m-30) cc_final: 0.7829 (m-30) REVERT: E 22 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.7011 (m-30) REVERT: K 66 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8241 (tt) REVERT: K 187 VAL cc_start: 0.8280 (p) cc_final: 0.8056 (m) REVERT: F 3 GLU cc_start: 0.4271 (tm-30) cc_final: 0.3900 (mm-30) REVERT: F 132 GLU cc_start: 0.3059 (tm-30) cc_final: 0.2729 (mt-10) REVERT: F 301 MET cc_start: -0.0027 (ttm) cc_final: -0.1595 (ttm) REVERT: F 344 MET cc_start: 0.4019 (mmm) cc_final: 0.1993 (tmm) REVERT: F 391 MET cc_start: -0.0836 (ptm) cc_final: -0.1388 (ptm) outliers start: 54 outliers final: 28 residues processed: 313 average time/residue: 0.3593 time to fit residues: 167.8627 Evaluate side-chains 282 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 250 time to evaluate : 2.176 ------------------------------------------------------------------------------- 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 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 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 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 236 SER Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain K residue 47 LEU 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 228 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 189 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 128 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 203 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20798 Z= 0.162 Angle : 0.542 19.034 28316 Z= 0.271 Chirality : 0.042 0.203 3121 Planarity : 0.004 0.050 3463 Dihedral : 13.818 164.871 3467 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.39 % Allowed : 11.85 % Favored : 84.76 % 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: -2.18 (0.16), residues: 2325 helix: -0.65 (0.17), residues: 879 sheet: -1.59 (0.26), residues: 342 loop : -2.02 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 152 HIS 0.005 0.001 HIS A 60 PHE 0.015 0.001 PHE C 276 TYR 0.018 0.001 TYR K 224 ARG 0.005 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 330 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 264 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6872 (tm-30) REVERT: A 600 PHE cc_start: 0.7613 (t80) cc_final: 0.7345 (t80) REVERT: B 123 MET cc_start: 0.4370 (OUTLIER) cc_final: 0.4037 (ttt) REVERT: B 152 MET cc_start: 0.6617 (mtm) cc_final: 0.5703 (mmt) REVERT: C 233 TYR cc_start: 0.8212 (m-10) cc_final: 0.7887 (m-80) REVERT: C 276 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6806 (m-80) REVERT: D 64 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7617 (mm-30) REVERT: D 184 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7146 (tt0) REVERT: E 22 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: K 267 LYS cc_start: 0.7544 (mmmt) cc_final: 0.6938 (tttt) REVERT: F 3 GLU cc_start: 0.4075 (tm-30) cc_final: 0.3818 (mm-30) REVERT: F 301 MET cc_start: -0.0108 (ttm) cc_final: -0.1681 (ttm) REVERT: F 344 MET cc_start: 0.4043 (mmm) cc_final: 0.1987 (tmm) REVERT: F 391 MET cc_start: -0.0834 (ptm) cc_final: -0.1369 (ptm) outliers start: 66 outliers final: 33 residues processed: 309 average time/residue: 0.3782 time to fit residues: 172.7320 Evaluate side-chains 281 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 244 time to evaluate : 2.206 ------------------------------------------------------------------------------- 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 365 VAL 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 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 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 184 GLU 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 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 236 SER Chi-restraints excluded: chain E residue 244 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 164 GLU Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 222 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 169 optimal weight: 9.9990 chunk 115 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 140 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 183 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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** D 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20798 Z= 0.218 Angle : 0.568 14.167 28316 Z= 0.283 Chirality : 0.043 0.250 3121 Planarity : 0.004 0.050 3463 Dihedral : 13.765 162.867 3467 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.72 % Allowed : 13.55 % Favored : 83.74 % 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: -1.93 (0.17), residues: 2325 helix: -0.40 (0.18), residues: 889 sheet: -1.37 (0.27), residues: 338 loop : -1.97 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 156 HIS 0.006 0.001 HIS A 60 PHE 0.019 0.001 PHE A 59 TYR 0.018 0.001 TYR K 224 ARG 0.005 0.000 ARG A 223 *********************** 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 307 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 254 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7327 (mtp-110) cc_final: 0.6866 (ttm110) REVERT: A 532 MET cc_start: 0.8591 (mpp) cc_final: 0.8260 (mmm) REVERT: A 545 MET cc_start: 0.8254 (tpp) cc_final: 0.8003 (tpp) REVERT: A 558 GLU cc_start: 0.7237 (tm-30) cc_final: 0.7035 (tm-30) REVERT: A 600 PHE cc_start: 0.7753 (t80) cc_final: 0.7436 (t80) REVERT: B 123 MET cc_start: 0.4513 (OUTLIER) cc_final: 0.4259 (ttt) REVERT: B 152 MET cc_start: 0.6641 (mtm) cc_final: 0.5718 (mmt) REVERT: C 26 GLN cc_start: 0.6745 (pm20) cc_final: 0.6433 (pm20) REVERT: C 233 TYR cc_start: 0.8108 (m-80) cc_final: 0.7763 (m-10) REVERT: C 276 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6861 (m-80) REVERT: D 64 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7609 (mm-30) REVERT: D 184 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: E 22 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.7036 (m-30) REVERT: F 3 GLU cc_start: 0.4087 (tm-30) cc_final: 0.3738 (mm-30) REVERT: F 301 MET cc_start: -0.0123 (ttm) cc_final: -0.1668 (ttm) REVERT: F 344 MET cc_start: 0.4382 (mmm) cc_final: 0.2232 (tmm) REVERT: F 391 MET cc_start: -0.0476 (ptm) cc_final: -0.0809 (ptm) outliers start: 53 outliers final: 39 residues processed: 288 average time/residue: 0.3677 time to fit residues: 156.4546 Evaluate side-chains 285 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 242 time to evaluate : 2.070 ------------------------------------------------------------------------------- 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 504 GLU 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 764 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 126 LEU 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 83 ASN 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 236 SER Chi-restraints excluded: chain E residue 244 MET 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 164 GLU Chi-restraints excluded: chain K residue 228 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 68 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 40 optimal weight: 0.4980 chunk 119 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 204 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 E 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20798 Z= 0.152 Angle : 0.533 12.861 28316 Z= 0.264 Chirality : 0.042 0.214 3121 Planarity : 0.004 0.046 3463 Dihedral : 13.687 166.478 3467 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.67 % Allowed : 13.90 % Favored : 83.43 % 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: -1.57 (0.17), residues: 2325 helix: -0.05 (0.18), residues: 888 sheet: -1.19 (0.28), residues: 319 loop : -1.81 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 290 HIS 0.005 0.001 HIS A 60 PHE 0.044 0.001 PHE A 561 TYR 0.016 0.001 TYR K 224 ARG 0.005 0.000 ARG F 212 *********************** 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 324 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 272 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 ARG cc_start: 0.7273 (mtp180) cc_final: 0.6930 (mmm160) REVERT: A 545 MET cc_start: 0.8283 (tpp) cc_final: 0.7975 (tpp) REVERT: A 558 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6951 (tm-30) REVERT: A 600 PHE cc_start: 0.7669 (t80) cc_final: 0.7387 (t80) REVERT: A 692 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7664 (t0) REVERT: B 123 MET cc_start: 0.4313 (OUTLIER) cc_final: 0.4042 (ttt) REVERT: B 152 MET cc_start: 0.6576 (mtm) cc_final: 0.5694 (mmt) REVERT: C 64 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7950 (mt-10) REVERT: C 276 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6743 (m-80) REVERT: D 64 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7404 (mm-30) REVERT: D 184 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7124 (tt0) REVERT: E 22 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.7048 (m-30) REVERT: E 128 ASP cc_start: 0.7713 (p0) cc_final: 0.7346 (p0) REVERT: E 203 LYS cc_start: 0.7889 (ttpp) cc_final: 0.7688 (ttpp) REVERT: K 183 ASN cc_start: 0.6926 (t0) cc_final: 0.6707 (t0) REVERT: K 267 LYS cc_start: 0.7493 (mmmt) cc_final: 0.7059 (tttt) REVERT: F 3 GLU cc_start: 0.4161 (OUTLIER) cc_final: 0.3947 (mp0) REVERT: F 301 MET cc_start: 0.0590 (ttm) cc_final: -0.1101 (ttm) REVERT: F 344 MET cc_start: 0.4293 (mmm) cc_final: 0.2148 (tmm) REVERT: F 391 MET cc_start: -0.0469 (ptm) cc_final: -0.0814 (ptm) REVERT: F 397 GLU cc_start: 0.4794 (pp20) cc_final: 0.3556 (tt0) outliers start: 52 outliers final: 40 residues processed: 303 average time/residue: 0.3812 time to fit residues: 171.8571 Evaluate side-chains 296 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 250 time to evaluate : 2.679 ------------------------------------------------------------------------------- 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 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 504 GLU 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 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 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 184 GLU 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 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 236 SER Chi-restraints excluded: chain E residue 244 MET 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 62 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 3 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 196 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 116 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 203 optimal weight: 0.3980 chunk 127 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20798 Z= 0.140 Angle : 0.515 12.996 28316 Z= 0.256 Chirality : 0.041 0.197 3121 Planarity : 0.004 0.048 3463 Dihedral : 13.617 170.352 3467 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.77 % Allowed : 14.01 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.17), residues: 2325 helix: 0.16 (0.18), residues: 894 sheet: -1.11 (0.28), residues: 317 loop : -1.66 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 290 HIS 0.005 0.001 HIS A 60 PHE 0.037 0.001 PHE A 561 TYR 0.014 0.001 TYR K 224 ARG 0.006 0.000 ARG D 181 *********************** 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 319 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 265 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7718 (mtm180) REVERT: A 375 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7735 (mmmt) REVERT: A 524 ARG cc_start: 0.7261 (mtp180) cc_final: 0.6895 (mmm160) REVERT: A 545 MET cc_start: 0.8302 (tpp) cc_final: 0.7980 (tpp) REVERT: A 558 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6975 (tm-30) REVERT: A 600 PHE cc_start: 0.7666 (t80) cc_final: 0.7334 (t80) REVERT: A 692 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7650 (t0) REVERT: B 152 MET cc_start: 0.6388 (mtm) cc_final: 0.5647 (mmt) REVERT: C 64 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7884 (mt-10) REVERT: C 276 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6763 (m-80) REVERT: D 184 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: E 22 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7112 (m-30) REVERT: E 128 ASP cc_start: 0.7674 (p0) cc_final: 0.7313 (p0) REVERT: K 183 ASN cc_start: 0.6881 (t0) cc_final: 0.6606 (t0) REVERT: K 237 LYS cc_start: 0.6349 (tptp) cc_final: 0.6139 (tttt) REVERT: K 267 LYS cc_start: 0.7473 (mmmt) cc_final: 0.6993 (tttt) REVERT: F 301 MET cc_start: 0.0426 (ttm) cc_final: -0.1212 (ttm) REVERT: F 344 MET cc_start: 0.4276 (mmm) cc_final: 0.2115 (tmm) REVERT: F 391 MET cc_start: -0.0039 (ptm) cc_final: -0.0373 (ptm) REVERT: F 397 GLU cc_start: 0.4859 (pp20) cc_final: 0.3887 (tt0) outliers start: 54 outliers final: 36 residues processed: 298 average time/residue: 0.3550 time to fit residues: 156.7141 Evaluate side-chains 286 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 246 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 386 LEU 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 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 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 236 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 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 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 236 SER Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain E residue 260 MET 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 222 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 125 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 121 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 0.1980 chunk 184 optimal weight: 5.9990 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 C 183 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** 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: 0.7425 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20798 Z= 0.150 Angle : 0.530 13.527 28316 Z= 0.261 Chirality : 0.042 0.241 3121 Planarity : 0.004 0.046 3463 Dihedral : 13.565 170.219 3466 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.36 % Allowed : 14.83 % Favored : 82.81 % 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: -1.14 (0.17), residues: 2325 helix: 0.32 (0.18), residues: 892 sheet: -1.00 (0.29), residues: 312 loop : -1.57 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 131 HIS 0.005 0.001 HIS A 60 PHE 0.038 0.001 PHE A 561 TYR 0.016 0.001 TYR K 224 ARG 0.007 0.000 ARG D 181 *********************** 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 302 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 256 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7973 (mtm-85) cc_final: 0.7736 (mtm180) REVERT: A 65 MET cc_start: 0.4888 (ttm) cc_final: 0.4078 (mtp) REVERT: A 375 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7748 (mmmt) REVERT: A 524 ARG cc_start: 0.7264 (mtp180) cc_final: 0.6892 (mmm160) REVERT: A 545 MET cc_start: 0.8301 (tpp) cc_final: 0.7984 (tpp) REVERT: A 558 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6868 (tm-30) REVERT: A 600 PHE cc_start: 0.7656 (t80) cc_final: 0.7321 (t80) REVERT: A 692 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7681 (t0) REVERT: B 152 MET cc_start: 0.6376 (mtm) cc_final: 0.5620 (mmt) REVERT: B 164 ASN cc_start: 0.2709 (OUTLIER) cc_final: 0.2508 (p0) REVERT: C 64 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7883 (mt-10) REVERT: C 276 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6857 (m-80) REVERT: D 184 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7026 (tt0) REVERT: E 22 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: E 89 ARG cc_start: 0.6991 (ptm-80) cc_final: 0.5190 (ptt180) REVERT: E 128 ASP cc_start: 0.7703 (p0) cc_final: 0.7327 (p0) REVERT: J 101 MET cc_start: 0.2081 (tpp) cc_final: 0.1878 (tpp) REVERT: K 164 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6203 (tt0) REVERT: K 183 ASN cc_start: 0.6784 (t0) cc_final: 0.6494 (t0) REVERT: K 237 LYS cc_start: 0.6391 (tptp) cc_final: 0.6127 (tttt) REVERT: K 267 LYS cc_start: 0.7631 (mmmt) cc_final: 0.7164 (tttt) REVERT: F 301 MET cc_start: 0.0733 (ttm) cc_final: -0.0974 (ttm) REVERT: F 344 MET cc_start: 0.4290 (mmm) cc_final: 0.1556 (tmm) REVERT: F 391 MET cc_start: -0.0161 (ptm) cc_final: -0.0489 (ptm) outliers start: 46 outliers final: 36 residues processed: 284 average time/residue: 0.3457 time to fit residues: 147.1074 Evaluate side-chains 289 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 248 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 386 LEU 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 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 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 164 ASN 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 236 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 151 GLU 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 236 SER Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain E residue 260 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 194 optimal weight: 3.9990 chunk 177 optimal weight: 0.4980 chunk 189 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 171 optimal weight: 0.2980 chunk 179 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN C 183 ASN C 205 HIS D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20798 Z= 0.155 Angle : 0.530 13.570 28316 Z= 0.262 Chirality : 0.042 0.233 3121 Planarity : 0.004 0.046 3463 Dihedral : 13.541 169.896 3466 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.41 % Allowed : 14.67 % Favored : 82.91 % 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: -1.09 (0.17), residues: 2325 helix: 0.33 (0.18), residues: 898 sheet: -0.95 (0.29), residues: 312 loop : -1.52 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 596 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 0.005 0.000 ARG A 223 *********************** 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 304 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 257 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7754 (mtm180) REVERT: A 65 MET cc_start: 0.4830 (ttm) cc_final: 0.4025 (mtp) REVERT: A 545 MET cc_start: 0.8275 (tpp) cc_final: 0.7966 (tpp) REVERT: A 558 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6889 (tm-30) REVERT: A 600 PHE cc_start: 0.7652 (t80) cc_final: 0.7320 (t80) REVERT: A 692 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7664 (t0) REVERT: B 152 MET cc_start: 0.6371 (mtm) cc_final: 0.5546 (mmt) REVERT: B 153 LEU cc_start: 0.5652 (mm) cc_final: 0.4773 (tp) REVERT: C 276 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6868 (m-80) REVERT: D 184 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: E 22 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7094 (m-30) REVERT: E 89 ARG cc_start: 0.6977 (ptm-80) cc_final: 0.5202 (ptt180) REVERT: E 128 ASP cc_start: 0.7709 (p0) cc_final: 0.7326 (p0) REVERT: K 164 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6272 (tt0) REVERT: K 183 ASN cc_start: 0.6735 (t0) cc_final: 0.6442 (t0) REVERT: K 237 LYS cc_start: 0.6436 (tptp) cc_final: 0.6139 (tttt) REVERT: K 267 LYS cc_start: 0.7644 (mmmt) cc_final: 0.7183 (tttt) REVERT: F 301 MET cc_start: 0.0705 (ttm) cc_final: -0.0993 (ttm) REVERT: F 344 MET cc_start: 0.4365 (mmm) cc_final: 0.1572 (tmm) REVERT: F 391 MET cc_start: -0.0100 (ptm) cc_final: -0.0423 (ptm) REVERT: F 397 GLU cc_start: 0.4547 (pp20) cc_final: 0.3370 (tp30) outliers start: 47 outliers final: 39 residues processed: 285 average time/residue: 0.3463 time to fit residues: 148.1960 Evaluate side-chains 288 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 245 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 386 LEU 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 579 ASP 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 761 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 236 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 151 GLU 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 236 SER Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain E residue 260 MET 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 228 SER Chi-restraints excluded: chain F residue 222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 200 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 139 optimal weight: 0.0980 chunk 210 optimal weight: 0.5980 chunk 193 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 205 HIS ** 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: 0.7420 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20798 Z= 0.148 Angle : 0.535 13.258 28316 Z= 0.264 Chirality : 0.042 0.305 3121 Planarity : 0.004 0.046 3463 Dihedral : 13.501 170.161 3466 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.21 % Allowed : 14.93 % Favored : 82.86 % 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: -0.95 (0.18), residues: 2325 helix: 0.45 (0.18), residues: 890 sheet: -0.81 (0.30), residues: 298 loop : -1.46 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 596 HIS 0.006 0.001 HIS A 380 PHE 0.036 0.001 PHE A 561 TYR 0.016 0.001 TYR K 250 ARG 0.007 0.000 ARG D 181 ********************** 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 295 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 252 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.4756 (ttm) cc_final: 0.3993 (mtp) REVERT: A 545 MET cc_start: 0.8329 (tpp) cc_final: 0.8026 (tpp) REVERT: A 558 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6863 (tm-30) REVERT: A 600 PHE cc_start: 0.7661 (t80) cc_final: 0.7321 (t80) REVERT: A 692 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7663 (t0) REVERT: B 152 MET cc_start: 0.6277 (mtm) cc_final: 0.5504 (mmt) REVERT: B 153 LEU cc_start: 0.5506 (mm) cc_final: 0.4737 (tp) REVERT: C 276 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6888 (m-80) REVERT: D 184 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7008 (tt0) REVERT: E 22 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7142 (m-30) REVERT: E 128 ASP cc_start: 0.7721 (p0) cc_final: 0.7348 (p0) REVERT: K 164 GLU cc_start: 0.6930 (tm-30) cc_final: 0.6315 (tt0) REVERT: K 237 LYS cc_start: 0.6458 (tptp) cc_final: 0.6173 (tttt) REVERT: K 267 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7199 (tttt) REVERT: F 301 MET cc_start: 0.0695 (ttm) cc_final: -0.0994 (ttm) REVERT: F 391 MET cc_start: -0.0070 (ptm) cc_final: -0.0397 (ptm) REVERT: F 397 GLU cc_start: 0.4532 (pp20) cc_final: 0.3494 (tp30) outliers start: 43 outliers final: 38 residues processed: 277 average time/residue: 0.3621 time to fit residues: 149.7945 Evaluate side-chains 283 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 241 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 386 LEU 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 579 ASP 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 761 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 236 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 151 GLU 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 236 SER Chi-restraints excluded: chain E residue 244 MET 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 228 SER Chi-restraints excluded: chain F residue 222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 172 optimal weight: 0.0470 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN D 136 ASN D 179 ASN K 183 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.202569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155044 restraints weight = 25325.612| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.42 r_work: 0.3203 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20798 Z= 0.161 Angle : 0.531 13.196 28316 Z= 0.263 Chirality : 0.042 0.262 3121 Planarity : 0.004 0.046 3463 Dihedral : 13.436 169.475 3466 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.36 % Allowed : 14.93 % Favored : 82.71 % 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: -0.90 (0.18), residues: 2325 helix: 0.52 (0.18), residues: 887 sheet: -0.77 (0.30), residues: 298 loop : -1.45 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 596 HIS 0.004 0.001 HIS A 60 PHE 0.037 0.001 PHE A 561 TYR 0.016 0.001 TYR K 250 ARG 0.006 0.000 ARG C 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4547.65 seconds wall clock time: 82 minutes 54.14 seconds (4974.14 seconds total)