Starting phenix.real_space_refine on Fri Feb 16 22:58:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muu_9256/02_2024/6muu_9256_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muu_9256/02_2024/6muu_9256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muu_9256/02_2024/6muu_9256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muu_9256/02_2024/6muu_9256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muu_9256/02_2024/6muu_9256_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muu_9256/02_2024/6muu_9256_neut.pdb" } resolution = 3.0 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= 0.007 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 3 6.06 5 P 24 5.49 5 S 49 5.16 5 C 10573 2.51 5 N 2925 2.21 5 O 3142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 47": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" 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 687": "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 96": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 334": "NH1" <-> "NH2" Residue "F ARG 383": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16716 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6211 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 36, 'TRANS': 743} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 941 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 100 Chain: "C" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2202 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 12, 'TRANS': 263} Chain breaks: 1 Chain: "D" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2254 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain breaks: 1 Chain: "E" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2257 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 20, 'TRANS': 264} Chain: "F" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2302 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 16, 'TRANS': 306} Chain breaks: 13 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 338 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 183 Chain: "G" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 546 Classifications: {'RNA': 25} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p_pur': 8, 'rna3p_pyr': 4} Link IDs: {'rna2p': 13, 'rna3p': 11} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3135 SG CYS A 389 46.938 73.949 98.475 1.00 37.02 S ATOM 3155 SG CYS A 392 44.894 70.349 97.471 1.00 35.05 S ATOM 3310 SG CYS A 413 45.189 71.721 101.524 1.00 38.54 S ATOM 7967 SG CYS C 113 54.582 99.125 83.196 1.00 38.63 S ATOM 8034 SG CYS C 122 55.964 100.205 79.685 1.00 28.96 S ATOM 8054 SG CYS C 125 54.673 96.603 80.577 1.00 28.10 S ATOM 10221 SG CYS D 113 85.911 85.116 80.930 1.00 41.91 S ATOM 10288 SG CYS D 122 88.208 87.178 78.386 1.00 45.54 S ATOM 10308 SG CYS D 125 84.793 84.588 77.509 1.00 38.51 S Time building chain proxies: 9.42, per 1000 atoms: 0.56 Number of scatterers: 16716 At special positions: 0 Unit cell: (137.214, 124.146, 145.926, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 49 16.00 P 24 15.00 O 3142 8.00 N 2925 7.00 C 10573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.61 Conformation dependent library (CDL) restraints added in 3.0 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 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 392 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 111 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 125 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 122 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 111 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 125 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 113 " Number of angles added : 6 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3810 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 28 sheets defined 43.2% alpha, 14.5% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.579A pdb=" N LEU A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 23 removed outlier: 3.651A pdb=" N VAL A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 49 through 59 removed outlier: 4.555A pdb=" N LEU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.594A pdb=" N ALA A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 removed outlier: 3.728A pdb=" N GLU A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 183 Proline residue: A 177 - end of helix removed outlier: 3.631A 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 219 through 224 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.606A pdb=" N TYR A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.607A pdb=" N ALA A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 325 removed outlier: 3.541A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.557A pdb=" N LYS A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.566A pdb=" N ASN A 417 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 420 " --> pdb=" O CYS A 416 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.576A pdb=" N ARG A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.793A pdb=" N ILE A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 596 through 614 removed outlier: 3.635A pdb=" N GLU A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 645 removed outlier: 3.532A pdb=" N ASP A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 650 removed outlier: 4.163A pdb=" N GLU A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 688 removed outlier: 3.537A pdb=" N ALA A 685 " --> pdb=" O TRP A 681 " (cutoff:3.500A) Proline residue: A 686 - end of helix Processing helix chain 'A' and resid 702 through 719 removed outlier: 3.575A pdb=" N LEU A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TRP A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 736 removed outlier: 3.807A pdb=" N LEU A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 729 " --> pdb=" O TRP A 725 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 746 removed outlier: 3.741A pdb=" N VAL A 746 " --> pdb=" O PRO A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 755 removed outlier: 3.855A pdb=" N ARG A 755 " --> pdb=" O LYS A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 775 removed outlier: 4.246A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 44 removed outlier: 3.865A pdb=" N MET B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.961A pdb=" N GLN B 53 " --> pdb=" O TRP B 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 49 through 53' Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.552A pdb=" N ALA B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 88 removed outlier: 3.692A pdb=" N LEU B 75 " --> pdb=" O PRO B 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN B 88 " --> pdb=" O TYR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 110 removed outlier: 4.071A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 105 " --> pdb=" O MET B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 141 through 158 removed outlier: 3.566A pdb=" N PHE B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 3.516A pdb=" N VAL B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 183 removed outlier: 3.696A pdb=" N ASN B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 182 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 69 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.675A pdb=" N ALA C 82 " --> pdb=" O PRO C 79 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 84 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 205 through 220 Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.810A pdb=" N TYR C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 280 removed outlier: 3.702A pdb=" N SER C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'D' and resid 51 through 69 removed outlier: 3.523A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.902A pdb=" N LEU D 127 " --> pdb=" O PRO D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 159 removed outlier: 3.710A pdb=" N GLU D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP D 156 " --> pdb=" O TRP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 221 removed outlier: 4.032A pdb=" N ASP D 209 " --> pdb=" O HIS D 205 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 254 removed outlier: 3.563A pdb=" N ARG D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 273 removed outlier: 3.902A pdb=" N ILE D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.833A pdb=" N LYS D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 36 removed outlier: 3.625A pdb=" N ALA E 27 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 50 removed outlier: 3.581A pdb=" N VAL E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.847A pdb=" N VAL E 73 " --> pdb=" O PRO E 70 " (cutoff:3.500A) removed outlier: 4.024A 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 Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.657A pdb=" N LEU E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 removed outlier: 3.557A pdb=" N GLY E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 182 removed outlier: 3.872A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'F' and resid 36 through 46 removed outlier: 3.521A pdb=" N LEU F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP F 43 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN F 46 " --> pdb=" O ASN F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 60 removed outlier: 3.674A pdb=" N ASN F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 113 through 133 removed outlier: 3.585A pdb=" N GLY F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 160 through 169 removed outlier: 3.570A pdb=" N MET F 165 " --> pdb=" O LEU F 161 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 183 removed outlier: 4.126A pdb=" N LEU F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 204 removed outlier: 3.629A pdb=" N ARG F 203 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 263 removed outlier: 3.577A pdb=" N ARG F 261 " --> pdb=" O THR F 257 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 277 Processing helix chain 'F' and resid 280 through 305 removed outlier: 4.927A pdb=" N GLU F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR F 297 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA F 299 " --> pdb=" O GLU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 324 removed outlier: 3.679A pdb=" N PHE F 321 " --> pdb=" O GLN F 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA F 323 " --> pdb=" O ARG F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 345 Processing helix chain 'F' and resid 346 through 349 Processing helix chain 'F' and resid 357 through 364 removed outlier: 3.946A pdb=" N LYS F 363 " --> pdb=" O ASN F 359 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 120 removed outlier: 4.345A pdb=" N LEU A 119 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.614A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 6.410A 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 386 through 388 Processing sheet with id=AA5, first strand: chain 'A' and resid 402 through 403 Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.619A pdb=" N GLY A 431 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE A 465 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR A 485 " --> pdb=" O ILE A 465 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL A 467 " --> pdb=" O TYR A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 580 through 584 removed outlier: 6.678A pdb=" N PHE A 591 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU A 620 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE A 656 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL A 622 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 689 through 691 removed outlier: 6.399A pdb=" N ARG A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 141 through 143 removed outlier: 4.064A pdb=" N PHE C 147 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.532A pdb=" N GLY C 13 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY C 7 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS C 14 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N PHE C 240 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS C 16 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE C 238 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 88 removed outlier: 5.080A pdb=" N SER C 85 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE C 101 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLY C 87 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AB4, first strand: chain 'C' and resid 163 through 168 Processing sheet with id=AB5, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.674A pdb=" N PHE D 147 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.635A pdb=" N GLY D 13 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS D 8 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE D 245 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL D 10 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE D 243 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS D 12 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE D 243 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 85 through 88 removed outlier: 5.327A pdb=" N SER D 85 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N PHE D 101 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLY D 87 " --> pdb=" O PHE D 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 104 Processing sheet with id=AB9, first strand: chain 'D' and resid 163 through 171 Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 61 removed outlier: 5.657A pdb=" N ILE E 54 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER E 162 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER E 56 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU E 160 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 66 through 68 Processing sheet with id=AC3, first strand: chain 'E' and resid 124 through 131 Processing sheet with id=AC4, first strand: chain 'E' and resid 252 through 254 Processing sheet with id=AC5, first strand: chain 'E' and resid 229 through 236 removed outlier: 6.625A pdb=" N LEU E 230 " --> pdb=" O THR E 245 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N THR E 245 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS E 232 " --> pdb=" O ARG E 243 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG E 243 " --> pdb=" O LYS E 232 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY E 234 " --> pdb=" O LYS E 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 261 through 263 Processing sheet with id=AC7, first strand: chain 'F' and resid 248 through 251 removed outlier: 3.762A pdb=" N VAL F 251 " --> pdb=" O ARG F 4 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.729A pdb=" N ILE F 100 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 209 through 210 Processing sheet with id=AD1, first strand: chain 'F' and resid 223 through 226 613 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 5.20 Time building geometry restraints manager: 7.18 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: 4048 1.33 - 1.45: 3797 1.45 - 1.58: 9149 1.58 - 1.70: 49 1.70 - 1.82: 80 Bond restraints: 17123 Sorted by residual: bond pdb=" C GLU E 74 " pdb=" N PRO E 75 " ideal model delta sigma weight residual 1.335 1.388 -0.052 1.36e-02 5.41e+03 1.47e+01 bond pdb=" N GLU F 280 " pdb=" CA GLU F 280 " ideal model delta sigma weight residual 1.457 1.488 -0.032 9.10e-03 1.21e+04 1.21e+01 bond pdb=" N THR F 16 " pdb=" CA THR F 16 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.15e+01 bond pdb=" N GLY F 279 " pdb=" CA GLY F 279 " ideal model delta sigma weight residual 1.446 1.476 -0.030 9.70e-03 1.06e+04 9.65e+00 bond pdb=" N ILE F 197 " pdb=" CA ILE F 197 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.19e-02 7.06e+03 9.58e+00 ... (remaining 17118 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.62: 485 105.62 - 112.79: 8649 112.79 - 119.96: 6497 119.96 - 127.13: 7372 127.13 - 134.30: 259 Bond angle restraints: 23262 Sorted by residual: angle pdb=" N PRO F 61 " pdb=" CA PRO F 61 " pdb=" CB PRO F 61 " ideal model delta sigma weight residual 103.08 110.83 -7.75 9.70e-01 1.06e+00 6.39e+01 angle pdb=" CA GLY F 279 " pdb=" C GLY F 279 " pdb=" O GLY F 279 " ideal model delta sigma weight residual 122.22 117.31 4.91 6.50e-01 2.37e+00 5.70e+01 angle pdb=" N PRO F 62 " pdb=" CA PRO F 62 " pdb=" CB PRO F 62 " ideal model delta sigma weight residual 103.00 110.59 -7.59 1.10e+00 8.26e-01 4.76e+01 angle pdb=" N PRO F 191 " pdb=" CA PRO F 191 " pdb=" CB PRO F 191 " ideal model delta sigma weight residual 103.00 110.41 -7.41 1.10e+00 8.26e-01 4.54e+01 angle pdb=" C4' G G 21 " pdb=" C3' G G 21 " pdb=" O3' G G 21 " ideal model delta sigma weight residual 109.40 99.68 9.72 1.50e+00 4.44e-01 4.20e+01 ... (remaining 23257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 10093 35.12 - 70.24: 152 70.24 - 105.37: 8 105.37 - 140.49: 0 140.49 - 175.61: 2 Dihedral angle restraints: 10255 sinusoidal: 4309 harmonic: 5946 Sorted by residual: dihedral pdb=" O4' U G 2 " pdb=" C1' U G 2 " pdb=" N1 U G 2 " pdb=" C2 U G 2 " ideal model delta sinusoidal sigma weight residual -128.00 47.61 -175.61 1 1.70e+01 3.46e-03 6.63e+01 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 39.93 -167.93 1 1.70e+01 3.46e-03 6.57e+01 dihedral pdb=" C THR F 16 " pdb=" N THR F 16 " pdb=" CA THR F 16 " pdb=" CB THR F 16 " ideal model delta harmonic sigma weight residual -122.00 -139.81 17.81 0 2.50e+00 1.60e-01 5.08e+01 ... (remaining 10252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2336 0.112 - 0.224: 186 0.224 - 0.335: 25 0.335 - 0.447: 0 0.447 - 0.559: 1 Chirality restraints: 2548 Sorted by residual: chirality pdb=" CA THR F 16 " pdb=" N THR F 16 " pdb=" C THR F 16 " pdb=" CB THR F 16 " both_signs ideal model delta sigma weight residual False 2.53 1.97 0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" CA LYS A 257 " pdb=" N LYS A 257 " pdb=" C LYS A 257 " pdb=" CB LYS A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C1' C G 14 " pdb=" O4' C G 14 " pdb=" C2' C G 14 " pdb=" N1 C G 14 " both_signs ideal model delta sigma weight residual False 2.45 2.15 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 2545 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 264 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C GLU E 264 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU E 264 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU E 265 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 22 " 0.245 9.50e-02 1.11e+02 1.10e-01 7.40e+00 pdb=" NE ARG A 22 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 22 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 22 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 22 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 389 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 390 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 390 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 390 " 0.034 5.00e-02 4.00e+02 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 82 2.47 - 3.08: 9957 3.08 - 3.69: 25251 3.69 - 4.29: 37616 4.29 - 4.90: 62035 Nonbonded interactions: 134941 Sorted by model distance: nonbonded pdb=" O2' G G 22 " pdb=" O5' U G 23 " model vdw 1.866 2.440 nonbonded pdb=" O VAL F 34 " pdb=" CB ASP F 81 " model vdw 1.883 3.440 nonbonded pdb=" O2' U G 24 " pdb=" O4' U G 25 " model vdw 1.948 2.440 nonbonded pdb=" CB GLN A 114 " pdb=" NE ARG A 117 " model vdw 1.985 3.520 nonbonded pdb=" O2' U G 24 " pdb=" C6 U G 25 " model vdw 2.042 3.340 ... (remaining 134936 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' selection = (chain 'D' and (resid 4 through 26 or resid 35 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.410 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 51.190 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 17123 Z= 0.483 Angle : 1.042 13.064 23262 Z= 0.625 Chirality : 0.066 0.559 2548 Planarity : 0.008 0.110 2909 Dihedral : 12.492 175.609 6445 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.34 % Favored : 93.51 % Rotamer: Outliers : 0.67 % Allowed : 4.59 % Favored : 94.73 % Cbeta Deviations : 0.05 % 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: -4.66 (0.14), residues: 2035 helix: -4.18 (0.09), residues: 807 sheet: -1.11 (0.29), residues: 273 loop : -2.60 (0.16), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 131 HIS 0.008 0.002 HIS D 205 PHE 0.029 0.003 PHE E 15 TYR 0.037 0.003 TYR A 265 ARG 0.013 0.001 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 470 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7747 (mmp) cc_final: 0.7317 (mtt) REVERT: A 308 LYS cc_start: 0.8308 (tttt) cc_final: 0.7925 (mtpp) REVERT: A 411 LYS cc_start: 0.8487 (mptt) cc_final: 0.8226 (mmmm) REVERT: A 584 TYR cc_start: 0.7405 (t80) cc_final: 0.7081 (t80) REVERT: A 684 TYR cc_start: 0.7966 (m-80) cc_final: 0.7651 (m-80) REVERT: D 2 ASP cc_start: 0.6946 (t0) cc_final: 0.6673 (t70) REVERT: D 244 GLU cc_start: 0.7302 (tt0) cc_final: 0.7079 (tt0) REVERT: E 255 ASN cc_start: 0.7891 (t0) cc_final: 0.7606 (p0) REVERT: F 6 LEU cc_start: 0.6575 (pp) cc_final: 0.6309 (pp) REVERT: F 116 SER cc_start: 0.7960 (t) cc_final: 0.7406 (p) REVERT: F 287 ASP cc_start: 0.6360 (t70) cc_final: 0.5932 (m-30) REVERT: F 384 ARG cc_start: 0.6416 (mpp80) cc_final: 0.5907 (mtp180) outliers start: 11 outliers final: 2 residues processed: 476 average time/residue: 1.3914 time to fit residues: 729.9399 Evaluate side-chains 286 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 178 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 99 optimal weight: 0.0870 chunk 121 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 64 HIS A 102 ASN A 481 GLN A 676 HIS B 72 ASN C 179 ASN C 183 ASN C 205 HIS D 37 ASN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN D 202 ASN D 205 HIS F 18 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17123 Z= 0.214 Angle : 0.678 12.773 23262 Z= 0.346 Chirality : 0.045 0.192 2548 Planarity : 0.006 0.049 2909 Dihedral : 12.038 174.362 2683 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.04 % Allowed : 15.37 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.16), residues: 2035 helix: -2.22 (0.14), residues: 828 sheet: -0.85 (0.30), residues: 266 loop : -2.17 (0.17), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 131 HIS 0.004 0.001 HIS A 382 PHE 0.030 0.002 PHE C 280 TYR 0.018 0.002 TYR F 297 ARG 0.007 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 298 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8852 (t) REVERT: A 167 LYS cc_start: 0.8332 (mtpm) cc_final: 0.7855 (mmmt) REVERT: A 257 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8714 (mtmm) REVERT: A 308 LYS cc_start: 0.8103 (tttt) cc_final: 0.7746 (mtmt) REVERT: A 463 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7475 (pp20) REVERT: A 513 ARG cc_start: 0.7482 (ptm-80) cc_final: 0.6705 (mtp-110) REVERT: A 584 TYR cc_start: 0.7350 (t80) cc_final: 0.7097 (t80) REVERT: A 630 ARG cc_start: 0.8315 (ptt90) cc_final: 0.8023 (ptt90) REVERT: A 644 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8321 (tp) REVERT: D 2 ASP cc_start: 0.6966 (t0) cc_final: 0.6634 (t70) REVERT: D 92 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6898 (p0) REVERT: E 140 ASP cc_start: 0.8075 (m-30) cc_final: 0.7852 (m-30) REVERT: E 148 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7132 (tp30) REVERT: E 223 THR cc_start: 0.8993 (t) cc_final: 0.8757 (m) REVERT: E 255 ASN cc_start: 0.7982 (t0) cc_final: 0.7644 (p0) REVERT: F 116 SER cc_start: 0.7499 (t) cc_final: 0.7280 (p) REVERT: F 287 ASP cc_start: 0.6492 (t70) cc_final: 0.6051 (m-30) REVERT: F 302 LYS cc_start: 0.6484 (OUTLIER) cc_final: 0.6136 (pttp) REVERT: F 345 THR cc_start: 0.5834 (m) cc_final: 0.5471 (p) outliers start: 66 outliers final: 27 residues processed: 338 average time/residue: 1.2755 time to fit residues: 479.9009 Evaluate side-chains 272 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 239 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 302 LYS Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 333 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 0.0070 chunk 58 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 168 optimal weight: 0.0570 chunk 187 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 overall best weight: 1.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN D 94 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17123 Z= 0.299 Angle : 0.662 12.126 23262 Z= 0.334 Chirality : 0.046 0.202 2548 Planarity : 0.005 0.050 2909 Dihedral : 11.814 174.055 2681 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.47 % Allowed : 16.23 % Favored : 79.30 % 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: -2.14 (0.17), residues: 2035 helix: -1.07 (0.17), residues: 835 sheet: -0.65 (0.30), residues: 276 loop : -1.92 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 131 HIS 0.006 0.001 HIS A 382 PHE 0.025 0.002 PHE E 15 TYR 0.025 0.002 TYR A 265 ARG 0.008 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 250 time to evaluate : 1.951 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.7909 (mmp) cc_final: 0.7286 (mtt) REVERT: A 257 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8657 (mtmm) REVERT: A 463 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7544 (pp20) REVERT: A 584 TYR cc_start: 0.7445 (t80) cc_final: 0.7187 (t80) REVERT: A 644 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8309 (tp) REVERT: D 2 ASP cc_start: 0.7228 (t0) cc_final: 0.6818 (t70) REVERT: D 160 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6711 (mp0) REVERT: D 168 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7381 (mt-10) REVERT: D 193 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7806 (mm-30) REVERT: E 140 ASP cc_start: 0.8070 (m-30) cc_final: 0.7783 (m-30) REVERT: F 287 ASP cc_start: 0.6626 (t70) cc_final: 0.6132 (m-30) REVERT: F 344 MET cc_start: 0.5896 (OUTLIER) cc_final: 0.5489 (mmm) outliers start: 73 outliers final: 40 residues processed: 297 average time/residue: 1.2169 time to fit residues: 404.5054 Evaluate side-chains 283 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 238 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 344 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 189 optimal weight: 20.0000 chunk 201 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17123 Z= 0.346 Angle : 0.664 9.137 23262 Z= 0.336 Chirality : 0.047 0.253 2548 Planarity : 0.005 0.059 2909 Dihedral : 11.776 173.764 2681 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 5.76 % Allowed : 16.66 % Favored : 77.59 % 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: -1.76 (0.17), residues: 2035 helix: -0.60 (0.17), residues: 837 sheet: -0.63 (0.29), residues: 290 loop : -1.84 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 131 HIS 0.006 0.001 HIS A 382 PHE 0.019 0.002 PHE E 15 TYR 0.020 0.002 TYR A 265 ARG 0.005 0.001 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 236 time to evaluate : 1.809 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7627 (tp40) cc_final: 0.7420 (tm-30) REVERT: A 71 MET cc_start: 0.7993 (mmp) cc_final: 0.7457 (mtt) REVERT: A 167 LYS cc_start: 0.8431 (mtpp) cc_final: 0.7952 (mmmt) REVERT: A 257 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8672 (mtmm) REVERT: A 385 ARG cc_start: 0.6950 (mmp-170) cc_final: 0.6548 (mmm160) REVERT: A 411 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8035 (mtmm) REVERT: A 584 TYR cc_start: 0.7551 (t80) cc_final: 0.7268 (t80) REVERT: A 644 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8338 (tp) REVERT: A 724 ARG cc_start: 0.6091 (mtp85) cc_final: 0.5819 (mtp85) REVERT: C 75 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7314 (mtt90) REVERT: C 282 GLU cc_start: 0.6163 (tp30) cc_final: 0.5913 (tp30) REVERT: D 160 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6858 (mt-10) REVERT: D 243 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7912 (t80) REVERT: E 140 ASP cc_start: 0.8113 (m-30) cc_final: 0.7790 (m-30) REVERT: F 287 ASP cc_start: 0.6648 (t70) cc_final: 0.6167 (m-30) REVERT: F 344 MET cc_start: 0.5809 (OUTLIER) cc_final: 0.5415 (mmm) outliers start: 94 outliers final: 52 residues processed: 306 average time/residue: 1.2331 time to fit residues: 421.5544 Evaluate side-chains 287 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 229 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 243 PHE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 344 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 0.3980 chunk 180 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN B 77 ASN D 94 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17123 Z= 0.184 Angle : 0.597 11.169 23262 Z= 0.299 Chirality : 0.043 0.204 2548 Planarity : 0.004 0.063 2909 Dihedral : 11.707 174.706 2681 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.23 % Allowed : 18.31 % Favored : 77.46 % 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 (0.18), residues: 2035 helix: -0.06 (0.18), residues: 842 sheet: -0.62 (0.28), residues: 295 loop : -1.72 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 131 HIS 0.004 0.001 HIS D 111 PHE 0.012 0.001 PHE B 165 TYR 0.020 0.001 TYR E 124 ARG 0.008 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 252 time to evaluate : 1.831 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7604 (tp40) cc_final: 0.7343 (tm-30) REVERT: A 71 MET cc_start: 0.8030 (mmp) cc_final: 0.7541 (mtt) REVERT: A 167 LYS cc_start: 0.8374 (mtpp) cc_final: 0.7932 (mmmt) REVERT: A 411 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8092 (mtmm) REVERT: A 584 TYR cc_start: 0.7490 (t80) cc_final: 0.7252 (t80) REVERT: A 644 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8389 (tp) REVERT: A 724 ARG cc_start: 0.6054 (mtp85) cc_final: 0.5808 (mtp85) REVERT: A 751 LYS cc_start: 0.7789 (ttpt) cc_final: 0.7368 (mppt) REVERT: C 75 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7265 (mtt90) REVERT: D 2 ASP cc_start: 0.7150 (t0) cc_final: 0.6714 (t70) REVERT: D 92 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.6268 (p0) REVERT: D 120 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8396 (tt) REVERT: D 160 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6856 (mt-10) REVERT: D 243 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7949 (t80) REVERT: E 98 LYS cc_start: 0.8360 (tttt) cc_final: 0.8155 (ttpt) REVERT: E 140 ASP cc_start: 0.8083 (m-30) cc_final: 0.7826 (m-30) REVERT: E 223 THR cc_start: 0.9114 (t) cc_final: 0.8759 (m) REVERT: E 255 ASN cc_start: 0.7883 (t0) cc_final: 0.7532 (p0) REVERT: F 287 ASP cc_start: 0.6615 (t70) cc_final: 0.6126 (m-30) outliers start: 69 outliers final: 40 residues processed: 301 average time/residue: 1.2278 time to fit residues: 415.3289 Evaluate side-chains 277 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 231 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 243 PHE Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 0.7980 chunk 181 optimal weight: 40.0000 chunk 39 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 201 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN B 77 ASN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17123 Z= 0.188 Angle : 0.593 9.269 23262 Z= 0.295 Chirality : 0.044 0.301 2548 Planarity : 0.004 0.064 2909 Dihedral : 11.632 174.970 2681 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.90 % Favored : 94.05 % Rotamer: Outliers : 4.29 % Allowed : 18.86 % Favored : 76.85 % 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 (0.18), residues: 2035 helix: 0.19 (0.18), residues: 854 sheet: -0.59 (0.29), residues: 293 loop : -1.65 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 109 HIS 0.005 0.001 HIS A 382 PHE 0.016 0.001 PHE A 59 TYR 0.026 0.001 TYR A 26 ARG 0.008 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 246 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7527 (tp40) cc_final: 0.7290 (tm-30) REVERT: A 71 MET cc_start: 0.7912 (mmp) cc_final: 0.7590 (mtt) REVERT: A 167 LYS cc_start: 0.8343 (mtpp) cc_final: 0.7955 (ttpp) REVERT: A 255 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8332 (p) REVERT: A 411 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8120 (mtmm) REVERT: A 572 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7530 (ppp80) REVERT: A 584 TYR cc_start: 0.7518 (t80) cc_final: 0.7276 (t80) REVERT: A 630 ARG cc_start: 0.8197 (ptt90) cc_final: 0.7958 (ptt90) REVERT: A 644 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8387 (tp) REVERT: A 724 ARG cc_start: 0.6038 (mtp85) cc_final: 0.5787 (mtp85) REVERT: A 751 LYS cc_start: 0.7731 (ttpt) cc_final: 0.7301 (mppt) REVERT: A 773 MET cc_start: 0.7600 (mtm) cc_final: 0.6993 (ptp) REVERT: C 75 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7225 (mtt90) REVERT: D 92 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6093 (p0) REVERT: D 94 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.5984 (mt0) REVERT: D 120 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8395 (tt) REVERT: D 160 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6865 (mt-10) REVERT: D 243 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7949 (t80) REVERT: E 94 LYS cc_start: 0.8282 (ptpp) cc_final: 0.8068 (mtmt) REVERT: E 140 ASP cc_start: 0.8036 (m-30) cc_final: 0.7834 (m-30) REVERT: E 223 THR cc_start: 0.9121 (t) cc_final: 0.8769 (m) REVERT: E 255 ASN cc_start: 0.7884 (t0) cc_final: 0.7505 (p0) REVERT: F 287 ASP cc_start: 0.6592 (t70) cc_final: 0.6136 (m-30) outliers start: 70 outliers final: 41 residues processed: 296 average time/residue: 1.1984 time to fit residues: 397.0369 Evaluate side-chains 290 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 240 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 243 PHE Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 0.0770 chunk 22 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 125 optimal weight: 0.0030 chunk 122 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17123 Z= 0.241 Angle : 0.614 14.121 23262 Z= 0.304 Chirality : 0.045 0.245 2548 Planarity : 0.005 0.070 2909 Dihedral : 11.605 174.595 2681 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.41 % Allowed : 19.53 % Favored : 76.06 % 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: -0.96 (0.18), residues: 2035 helix: 0.37 (0.18), residues: 845 sheet: -0.54 (0.29), residues: 288 loop : -1.62 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 131 HIS 0.005 0.001 HIS A 382 PHE 0.012 0.001 PHE A 296 TYR 0.022 0.002 TYR E 124 ARG 0.008 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 243 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7516 (tp40) cc_final: 0.7301 (tm-30) REVERT: A 66 LYS cc_start: 0.7028 (mmpt) cc_final: 0.6826 (mmpt) REVERT: A 71 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7566 (mtt) REVERT: A 89 ASP cc_start: 0.7823 (m-30) cc_final: 0.7610 (m-30) REVERT: A 167 LYS cc_start: 0.8341 (mtpp) cc_final: 0.7953 (ttpp) REVERT: A 411 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8133 (mtmm) REVERT: A 572 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7446 (ppp80) REVERT: A 584 TYR cc_start: 0.7582 (t80) cc_final: 0.7339 (t80) REVERT: A 630 ARG cc_start: 0.8230 (ptt90) cc_final: 0.7993 (ptt90) REVERT: A 644 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8437 (tp) REVERT: A 724 ARG cc_start: 0.6093 (mtp85) cc_final: 0.5819 (mtp85) REVERT: A 751 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7300 (mppt) REVERT: C 75 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7226 (mtt90) REVERT: D 92 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6045 (p0) REVERT: D 94 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5944 (mt0) REVERT: D 120 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8393 (tt) REVERT: D 145 ASP cc_start: 0.8450 (m-30) cc_final: 0.8224 (m-30) REVERT: D 160 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6822 (mt-10) REVERT: D 243 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7854 (t80) REVERT: E 140 ASP cc_start: 0.8051 (m-30) cc_final: 0.7816 (m-30) REVERT: E 223 THR cc_start: 0.9121 (t) cc_final: 0.8766 (m) REVERT: F 287 ASP cc_start: 0.6598 (t70) cc_final: 0.6140 (m-30) outliers start: 72 outliers final: 44 residues processed: 298 average time/residue: 1.1935 time to fit residues: 397.4008 Evaluate side-chains 285 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 232 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 243 PHE Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17123 Z= 0.188 Angle : 0.595 10.864 23262 Z= 0.294 Chirality : 0.043 0.214 2548 Planarity : 0.004 0.074 2909 Dihedral : 11.607 175.013 2681 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.10 % Allowed : 20.27 % Favored : 75.63 % 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: -0.82 (0.18), residues: 2035 helix: 0.52 (0.18), residues: 848 sheet: -0.53 (0.29), residues: 278 loop : -1.58 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 393 HIS 0.004 0.001 HIS A 382 PHE 0.013 0.001 PHE E 159 TYR 0.023 0.001 TYR E 124 ARG 0.006 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 250 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7532 (mtt) REVERT: A 89 ASP cc_start: 0.7808 (m-30) cc_final: 0.7593 (m-30) REVERT: A 99 GLU cc_start: 0.7764 (tp30) cc_final: 0.7294 (tp30) REVERT: A 167 LYS cc_start: 0.8296 (mtpp) cc_final: 0.8046 (ttpp) REVERT: A 228 ARG cc_start: 0.7715 (mtp-110) cc_final: 0.7153 (mpp-170) REVERT: A 255 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8333 (p) REVERT: A 411 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8117 (mtmm) REVERT: A 572 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7386 (ppp80) REVERT: A 584 TYR cc_start: 0.7560 (t80) cc_final: 0.7311 (t80) REVERT: A 630 ARG cc_start: 0.8195 (ptt90) cc_final: 0.7972 (ptt90) REVERT: A 644 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8447 (tp) REVERT: A 724 ARG cc_start: 0.6230 (mtp85) cc_final: 0.5866 (mtp85) REVERT: A 751 LYS cc_start: 0.7717 (ttpt) cc_final: 0.7295 (mppt) REVERT: A 773 MET cc_start: 0.7532 (mtm) cc_final: 0.7086 (ptp) REVERT: C 75 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7204 (mtt90) REVERT: C 90 ARG cc_start: 0.7609 (ttp80) cc_final: 0.7383 (ttp-110) REVERT: C 282 GLU cc_start: 0.6343 (tp30) cc_final: 0.6133 (tp30) REVERT: D 120 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8408 (tt) REVERT: D 160 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6827 (mt-10) REVERT: E 223 THR cc_start: 0.9099 (t) cc_final: 0.8762 (m) REVERT: E 255 ASN cc_start: 0.7862 (t0) cc_final: 0.7515 (p0) REVERT: F 287 ASP cc_start: 0.6561 (t70) cc_final: 0.6129 (m-30) outliers start: 67 outliers final: 41 residues processed: 302 average time/residue: 1.2313 time to fit residues: 416.7087 Evaluate side-chains 286 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 238 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 257 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 186 optimal weight: 0.0770 chunk 112 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17123 Z= 0.219 Angle : 0.613 12.961 23262 Z= 0.304 Chirality : 0.044 0.215 2548 Planarity : 0.004 0.074 2909 Dihedral : 11.595 174.907 2681 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.92 % Allowed : 20.64 % Favored : 75.44 % 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: -0.74 (0.18), residues: 2035 helix: 0.61 (0.18), residues: 841 sheet: -0.52 (0.29), residues: 278 loop : -1.52 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 393 HIS 0.004 0.001 HIS A 382 PHE 0.010 0.001 PHE B 165 TYR 0.024 0.001 TYR E 124 ARG 0.006 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 249 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7535 (mtt) REVERT: A 99 GLU cc_start: 0.7789 (tp30) cc_final: 0.7344 (tp30) REVERT: A 167 LYS cc_start: 0.8313 (mtpp) cc_final: 0.8069 (ttpp) REVERT: A 228 ARG cc_start: 0.7721 (mtp-110) cc_final: 0.7173 (mpp-170) REVERT: A 411 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8126 (mtmm) REVERT: A 572 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7284 (ppp80) REVERT: A 584 TYR cc_start: 0.7574 (t80) cc_final: 0.7307 (t80) REVERT: A 644 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8463 (tp) REVERT: A 724 ARG cc_start: 0.6253 (mtp85) cc_final: 0.5886 (mtp85) REVERT: A 765 ASP cc_start: 0.7628 (t0) cc_final: 0.7356 (t0) REVERT: A 773 MET cc_start: 0.7559 (mtm) cc_final: 0.7110 (ptp) REVERT: C 75 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7205 (mtt90) REVERT: C 282 GLU cc_start: 0.6259 (tp30) cc_final: 0.6048 (tp30) REVERT: D 92 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6124 (p0) REVERT: D 160 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6836 (mt-10) REVERT: D 195 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: E 94 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7566 (ptpp) REVERT: E 223 THR cc_start: 0.9108 (t) cc_final: 0.8771 (m) REVERT: E 255 ASN cc_start: 0.7855 (t0) cc_final: 0.7446 (p0) REVERT: F 287 ASP cc_start: 0.6558 (t70) cc_final: 0.6163 (m-30) outliers start: 64 outliers final: 51 residues processed: 297 average time/residue: 1.2021 time to fit residues: 400.5189 Evaluate side-chains 295 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 237 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 257 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 93 optimal weight: 0.0870 chunk 137 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 190 optimal weight: 0.5980 chunk 165 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17123 Z= 0.168 Angle : 0.597 13.025 23262 Z= 0.293 Chirality : 0.043 0.204 2548 Planarity : 0.004 0.072 2909 Dihedral : 11.597 175.427 2681 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.88 % Allowed : 21.98 % Favored : 75.14 % 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: -0.58 (0.19), residues: 2035 helix: 0.78 (0.19), residues: 841 sheet: -0.43 (0.30), residues: 276 loop : -1.47 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 393 HIS 0.003 0.001 HIS A 382 PHE 0.012 0.001 PHE E 159 TYR 0.027 0.001 TYR E 124 ARG 0.007 0.000 ARG E 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 256 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7664 (mtt) REVERT: A 99 GLU cc_start: 0.7767 (tp30) cc_final: 0.7292 (tp30) REVERT: A 167 LYS cc_start: 0.8344 (mtpp) cc_final: 0.8105 (ttpp) REVERT: A 228 ARG cc_start: 0.7745 (mtp-110) cc_final: 0.7172 (mpp-170) REVERT: A 255 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8233 (p) REVERT: A 411 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8123 (mtmm) REVERT: A 630 ARG cc_start: 0.8211 (ptt90) cc_final: 0.7961 (ptt90) REVERT: A 644 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8501 (tp) REVERT: A 714 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7312 (tp30) REVERT: A 724 ARG cc_start: 0.6236 (mtp85) cc_final: 0.5923 (mtp85) REVERT: A 751 LYS cc_start: 0.7725 (ttpt) cc_final: 0.7286 (mppt) REVERT: A 765 ASP cc_start: 0.7572 (t0) cc_final: 0.7330 (t0) REVERT: A 773 MET cc_start: 0.7446 (mtm) cc_final: 0.7044 (ptp) REVERT: C 90 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7648 (ttp-170) REVERT: D 160 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6827 (mt-10) REVERT: D 195 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: D 260 VAL cc_start: 0.8814 (m) cc_final: 0.8344 (t) REVERT: E 46 ASP cc_start: 0.7363 (m-30) cc_final: 0.7121 (m-30) REVERT: E 94 LYS cc_start: 0.7646 (mtmt) cc_final: 0.7357 (ptpp) REVERT: E 223 THR cc_start: 0.9080 (t) cc_final: 0.8755 (m) REVERT: F 287 ASP cc_start: 0.6439 (t70) cc_final: 0.6062 (m-30) outliers start: 47 outliers final: 36 residues processed: 289 average time/residue: 1.2314 time to fit residues: 397.5449 Evaluate side-chains 284 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 243 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 10 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.163074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125215 restraints weight = 21959.303| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.93 r_work: 0.3161 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17123 Z= 0.253 Angle : 0.639 12.466 23262 Z= 0.317 Chirality : 0.045 0.213 2548 Planarity : 0.005 0.073 2909 Dihedral : 11.567 174.542 2681 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.88 % Allowed : 22.17 % Favored : 74.95 % 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: -0.62 (0.18), residues: 2035 helix: 0.73 (0.19), residues: 838 sheet: -0.40 (0.30), residues: 276 loop : -1.49 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 393 HIS 0.005 0.001 HIS A 382 PHE 0.032 0.002 PHE A 59 TYR 0.024 0.001 TYR E 124 ARG 0.006 0.000 ARG B 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7067.39 seconds wall clock time: 125 minutes 31.95 seconds (7531.95 seconds total)