Starting phenix.real_space_refine on Sat Feb 17 05:20:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7e_0640/02_2024/6o7e_0640_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7e_0640/02_2024/6o7e_0640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7e_0640/02_2024/6o7e_0640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7e_0640/02_2024/6o7e_0640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7e_0640/02_2024/6o7e_0640_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7e_0640/02_2024/6o7e_0640_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 3 7.51 5 Zn 3 6.06 5 P 51 5.49 5 S 49 5.16 5 C 11025 2.51 5 N 3090 2.21 5 O 3385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "A ARG 755": "NH1" <-> "NH2" Residue "A ARG 776": "NH1" <-> "NH2" Residue "A ARG 777": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 4": "NH1" <-> "NH2" Residue "Y ARG 95": "NH1" <-> "NH2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y ARG 198": "NH1" <-> "NH2" Residue "Y ARG 203": "NH1" <-> "NH2" Residue "Y ARG 383": "NH1" <-> "NH2" Residue "Y ARG 384": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17606 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6150 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 35, 'TRANS': 735} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1128 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2214 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2262 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2261 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 20, 'TRANS': 265} Chain: "G" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 589 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 4, 'rna3p_pur': 10, 'rna3p_pyr': 4} Link IDs: {'rna2p': 12, 'rna3p': 14} Chain: "H" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 398 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna2p': 5, 'rna3p': 13} Chain: "Y" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2536 Classifications: {'peptide': 361} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 106} Link IDs: {'PTRANS': 15, 'TRANS': 345} Chain breaks: 10 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 93, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 146 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {' MN': 3, ' ZN': 1, 'ANP': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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 3074 SG CYS A 389 37.892 75.781 90.435 1.00 31.85 S ATOM 3094 SG CYS A 392 37.312 71.986 89.324 1.00 29.62 S ATOM 3249 SG CYS A 413 36.293 73.674 92.950 1.00 39.63 S ATOM 3269 SG CYS A 416 39.468 72.026 92.600 1.00 40.77 S ATOM 8105 SG CYS C 113 35.937 101.845 73.782 1.00 32.07 S ATOM 8172 SG CYS C 122 37.047 103.593 70.619 1.00 24.93 S ATOM 8192 SG CYS C 125 37.319 98.974 71.753 1.00 28.16 S ATOM 10367 SG CYS D 113 69.676 102.898 77.101 1.00 44.46 S ATOM 10434 SG CYS D 122 71.311 105.673 74.810 1.00 40.17 S ATOM 10454 SG CYS D 125 69.883 101.685 73.673 1.00 35.09 S Time building chain proxies: 10.28, per 1000 atoms: 0.58 Number of scatterers: 17606 At special positions: 0 Unit cell: (133.947, 132.858, 137.214, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 Mn 3 24.99 S 49 16.00 P 51 15.00 O 3385 8.00 N 3090 7.00 C 11025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.07 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 416 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 413 " 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 125 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 111 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 122 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 125 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 113 " Number of angles added : 12 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 17 sheets defined 33.9% alpha, 11.5% beta 9 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 7.19 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.507A pdb=" N ALA A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 21 No H-bonds generated for 'chain 'A' and resid 18 through 21' Processing helix chain 'A' and resid 31 through 43 removed outlier: 3.502A pdb=" N ALA A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 53 No H-bonds generated for 'chain 'A' and resid 50 through 53' Processing helix chain 'A' and resid 72 through 77 removed outlier: 4.314A pdb=" N GLU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 87 through 103 removed outlier: 3.640A pdb=" N LEU A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.734A pdb=" N GLU A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.504A pdb=" N LEU A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.560A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 258 through 281 removed outlier: 3.986A pdb=" N SER A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 304 through 324 removed outlier: 3.722A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 367 removed outlier: 3.621A pdb=" N LYS A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 414 through 424 removed outlier: 4.352A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 420 " --> pdb=" O CYS A 416 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.502A pdb=" N SER A 530 " --> pdb=" O GLY A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 550 removed outlier: 3.567A pdb=" N ARG A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 557 No H-bonds generated for 'chain 'A' and resid 554 through 557' Processing helix chain 'A' and resid 562 through 565 No H-bonds generated for 'chain 'A' and resid 562 through 565' Processing helix chain 'A' and resid 596 through 613 removed outlier: 3.719A pdb=" N PHE A 600 " --> pdb=" O TRP A 596 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 646 removed outlier: 4.369A pdb=" N VAL A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 688 removed outlier: 3.553A pdb=" N ARG A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Proline residue: A 686 - end of helix Processing helix chain 'A' and resid 703 through 718 removed outlier: 3.583A pdb=" N LYS A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU A 711 " --> pdb=" O TRP A 707 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 732 removed outlier: 3.519A pdb=" N LEU A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 750 through 755 removed outlier: 3.586A pdb=" N GLU A 754 " --> pdb=" O THR A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 773 removed outlier: 4.283A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 40 No H-bonds generated for 'chain 'B' and resid 37 through 40' Processing helix chain 'B' and resid 49 through 62 Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 73 through 86 removed outlier: 3.684A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 109 removed outlier: 4.548A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 133 removed outlier: 3.806A pdb=" N VAL B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 155 removed outlier: 3.639A pdb=" N ALA B 144 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 3.595A pdb=" N VAL B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 removed outlier: 3.788A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 70 removed outlier: 3.858A pdb=" N ARG C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 119 No H-bonds generated for 'chain 'C' and resid 116 through 119' Processing helix chain 'C' and resid 150 through 157 removed outlier: 3.578A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 222 removed outlier: 3.729A pdb=" N ASP C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.500A pdb=" N ARG C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 248 through 253' Processing helix chain 'C' and resid 276 through 279 No H-bonds generated for 'chain 'C' and resid 276 through 279' Processing helix chain 'C' and resid 281 through 286 removed outlier: 3.521A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 68 removed outlier: 4.119A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 119 No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 150 through 158 removed outlier: 3.728A pdb=" N GLU D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 222 removed outlier: 3.595A pdb=" N ASP D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.761A pdb=" N ARG D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 276 through 279 No H-bonds generated for 'chain 'D' and resid 276 through 279' Processing helix chain 'D' and resid 281 through 284 No H-bonds generated for 'chain 'D' and resid 281 through 284' Processing helix chain 'E' and resid 21 through 35 removed outlier: 3.932A pdb=" N ALA E 27 " --> pdb=" O THR E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 50 removed outlier: 3.741A pdb=" N GLU E 42 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 77 through 80 No H-bonds generated for 'chain 'E' and resid 77 through 80' Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 104 through 110 removed outlier: 3.565A pdb=" N GLU E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.901A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 190 No H-bonds generated for 'chain 'E' and resid 188 through 190' Processing helix chain 'Y' and resid 22 through 24 No H-bonds generated for 'chain 'Y' and resid 22 through 24' Processing helix chain 'Y' and resid 37 through 43 removed outlier: 3.601A pdb=" N UNK Y 41 " --> pdb=" O THR Y 37 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N UNK Y 42 " --> pdb=" O GLU Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 59 removed outlier: 3.621A pdb=" N UNK Y 57 " --> pdb=" O UNK Y 53 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N UNK Y 58 " --> pdb=" O UNK Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 62 through 66 No H-bonds generated for 'chain 'Y' and resid 62 through 66' Processing helix chain 'Y' and resid 114 through 132 removed outlier: 3.934A pdb=" N GLY Y 119 " --> pdb=" O SER Y 115 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA Y 120 " --> pdb=" O SER Y 116 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE Y 121 " --> pdb=" O LEU Y 117 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA Y 124 " --> pdb=" O ALA Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 161 through 168 Processing helix chain 'Y' and resid 205 through 208 removed outlier: 3.754A pdb=" N ALA Y 208 " --> pdb=" O PRO Y 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 205 through 208' Processing helix chain 'Y' and resid 219 through 221 No H-bonds generated for 'chain 'Y' and resid 219 through 221' Processing helix chain 'Y' and resid 259 through 262 No H-bonds generated for 'chain 'Y' and resid 259 through 262' Processing helix chain 'Y' and resid 285 through 293 Processing helix chain 'Y' and resid 318 through 325 removed outlier: 3.558A pdb=" N SER Y 324 " --> pdb=" O SER Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 346 through 348 No H-bonds generated for 'chain 'Y' and resid 346 through 348' Processing helix chain 'Y' and resid 355 through 364 removed outlier: 3.631A pdb=" N VAL Y 360 " --> pdb=" O LYS Y 356 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS Y 363 " --> pdb=" O ASN Y 359 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 330 through 338 removed outlier: 3.610A pdb=" N PHE A 290 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 299 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL A 288 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 386 through 388 Processing sheet with id= C, first strand: chain 'A' and resid 442 through 445 removed outlier: 3.636A pdb=" N LEU A 443 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE A 451 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN A 481 " --> pdb=" O ILE A 465 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL A 467 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 483 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 620 through 627 removed outlier: 3.550A pdb=" N ASP A 589 " --> pdb=" O GLY A 586 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 593 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL A 582 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA A 595 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE A 580 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.723A pdb=" N GLY C 13 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY C 7 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER C 242 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS C 14 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE C 240 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS C 16 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N PHE C 238 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 163 through 171 removed outlier: 3.554A pdb=" N ARG C 185 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 7 through 12 removed outlier: 3.760A pdb=" N GLY D 7 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 13 through 17 Processing sheet with id= I, first strand: chain 'D' and resid 163 through 169 Processing sheet with id= J, first strand: chain 'E' and resid 195 through 203 removed outlier: 3.513A pdb=" N MET E 202 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 124 through 132 Processing sheet with id= L, first strand: chain 'E' and resid 212 through 214 Processing sheet with id= M, first strand: chain 'E' and resid 229 through 232 Processing sheet with id= N, first strand: chain 'E' and resid 261 through 263 Processing sheet with id= O, first strand: chain 'Y' and resid 248 through 251 removed outlier: 3.582A pdb=" N VAL Y 251 " --> pdb=" O ARG Y 4 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'Y' and resid 209 through 211 removed outlier: 3.577A pdb=" N HIS Y 254 " --> pdb=" O ILE Y 210 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'Y' and resid 236 through 243 removed outlier: 3.817A pdb=" N ILE Y 236 " --> pdb=" O VAL Y 229 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU Y 385 " --> pdb=" O GLU Y 228 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 5.53 Time building geometry restraints manager: 7.61 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: 4502 1.33 - 1.45: 3620 1.45 - 1.57: 9768 1.57 - 1.69: 100 1.69 - 1.81: 81 Bond restraints: 18071 Sorted by residual: bond pdb=" O3A ANP A 803 " pdb=" PB ANP A 803 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.22e+01 bond pdb=" O3A ANP A 802 " pdb=" PB ANP A 802 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" C ALA A 685 " pdb=" N PRO A 686 " ideal model delta sigma weight residual 1.334 1.385 -0.052 8.40e-03 1.42e+04 3.78e+01 bond pdb=" N3B ANP A 802 " pdb=" PG ANP A 802 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" N3B ANP A 803 " pdb=" PG ANP A 803 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.59e+01 ... (remaining 18066 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.97: 637 105.97 - 112.99: 9320 112.99 - 120.01: 6616 120.01 - 127.03: 7784 127.03 - 134.05: 299 Bond angle restraints: 24656 Sorted by residual: angle pdb=" C ARG E 53 " pdb=" N ILE E 54 " pdb=" CA ILE E 54 " ideal model delta sigma weight residual 122.27 128.82 -6.55 1.07e+00 8.73e-01 3.75e+01 angle pdb=" PB ANP A 802 " pdb=" N3B ANP A 802 " pdb=" PG ANP A 802 " ideal model delta sigma weight residual 126.95 109.02 17.93 3.00e+00 1.11e-01 3.57e+01 angle pdb=" PB ANP A 803 " pdb=" N3B ANP A 803 " pdb=" PG ANP A 803 " ideal model delta sigma weight residual 126.95 111.23 15.72 3.00e+00 1.11e-01 2.75e+01 angle pdb=" N GLY A 399 " pdb=" CA GLY A 399 " pdb=" C GLY A 399 " ideal model delta sigma weight residual 113.79 107.82 5.97 1.17e+00 7.31e-01 2.61e+01 angle pdb=" C GLU C 95 " pdb=" N ASN C 96 " pdb=" CA ASN C 96 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.28e+01 ... (remaining 24651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 10635 35.22 - 70.45: 211 70.45 - 105.67: 34 105.67 - 140.89: 0 140.89 - 176.11: 4 Dihedral angle restraints: 10884 sinusoidal: 4792 harmonic: 6092 Sorted by residual: dihedral pdb=" O4' C G 11 " pdb=" C1' C G 11 " pdb=" N1 C G 11 " pdb=" C2 C G 11 " ideal model delta sinusoidal sigma weight residual -128.00 48.11 -176.11 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C G 5 " pdb=" C1' C G 5 " pdb=" N1 C G 5 " pdb=" C2 C G 5 " ideal model delta sinusoidal sigma weight residual -128.00 43.10 -171.10 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" CA VAL A 775 " pdb=" C VAL A 775 " pdb=" N ARG A 776 " pdb=" CA ARG A 776 " ideal model delta harmonic sigma weight residual -180.00 -151.79 -28.21 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 10881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2129 0.059 - 0.117: 476 0.117 - 0.176: 95 0.176 - 0.235: 8 0.235 - 0.294: 6 Chirality restraints: 2714 Sorted by residual: chirality pdb=" C3' ANP A 802 " pdb=" C2' ANP A 802 " pdb=" C4' ANP A 802 " pdb=" O3' ANP A 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE E 122 " pdb=" CA ILE E 122 " pdb=" CG1 ILE E 122 " pdb=" CG2 ILE E 122 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C1' C G 5 " pdb=" O4' C G 5 " pdb=" C2' C G 5 " pdb=" N1 C G 5 " both_signs ideal model delta sigma weight residual False 2.45 2.19 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2711 not shown) Planarity restraints: 3007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 494 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO A 495 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 495 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 495 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 652 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.88e+00 pdb=" C ARG A 652 " -0.042 2.00e-02 2.50e+03 pdb=" O ARG A 652 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 653 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 173 " -0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO E 174 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " -0.033 5.00e-02 4.00e+02 ... (remaining 3004 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 80 2.50 - 3.10: 10938 3.10 - 3.70: 26893 3.70 - 4.30: 39621 4.30 - 4.90: 64726 Nonbonded interactions: 142258 Sorted by model distance: nonbonded pdb=" O2G ANP A 802 " pdb="MN MN A 805 " model vdw 1.896 2.320 nonbonded pdb=" OD1 ASP A 239 " pdb="MN MN A 806 " model vdw 1.943 2.320 nonbonded pdb=" OD2 ASP A 239 " pdb="MN MN A 806 " model vdw 1.957 2.320 nonbonded pdb=" O2A ANP A 802 " pdb="MN MN A 804 " model vdw 2.022 2.320 nonbonded pdb=" OD1 ASP A 588 " pdb="MN MN A 804 " model vdw 2.198 2.320 ... (remaining 142253 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 27 or resid 34 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.480 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 56.230 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 : 0.005 0.145 18071 Z= 0.316 Angle : 0.904 17.927 24656 Z= 0.484 Chirality : 0.052 0.294 2714 Planarity : 0.007 0.062 3007 Dihedral : 14.309 176.113 6990 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.24 % Allowed : 3.90 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (0.14), residues: 2018 helix: -4.40 (0.08), residues: 721 sheet: -2.64 (0.27), residues: 297 loop : -2.82 (0.16), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 131 HIS 0.006 0.001 HIS D 22 PHE 0.025 0.002 PHE C 194 TYR 0.020 0.002 TYR A 634 ARG 0.012 0.001 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 428 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7884 (tm130) cc_final: 0.7560 (tm-30) REVERT: A 41 LEU cc_start: 0.8942 (tp) cc_final: 0.8741 (tp) REVERT: A 386 LEU cc_start: 0.8472 (mp) cc_final: 0.8053 (mt) REVERT: A 507 MET cc_start: 0.7325 (mmm) cc_final: 0.6928 (mmm) REVERT: A 545 MET cc_start: 0.8252 (tpp) cc_final: 0.7799 (tpp) REVERT: A 571 LEU cc_start: 0.7573 (mm) cc_final: 0.7310 (mt) REVERT: B 178 TYR cc_start: 0.7070 (m-80) cc_final: 0.6613 (m-80) REVERT: C 47 LEU cc_start: 0.8667 (mt) cc_final: 0.8380 (mt) REVERT: D 133 LYS cc_start: 0.7103 (mppt) cc_final: 0.6768 (mtpp) REVERT: E 145 PHE cc_start: 0.8723 (m-80) cc_final: 0.8409 (m-80) REVERT: E 148 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6525 (mt-10) REVERT: E 176 MET cc_start: 0.8996 (mmm) cc_final: 0.8763 (mmt) REVERT: E 244 MET cc_start: 0.8080 (mtp) cc_final: 0.7573 (mtm) outliers start: 4 outliers final: 2 residues processed: 432 average time/residue: 0.4295 time to fit residues: 251.0838 Evaluate side-chains 218 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 216 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain E residue 53 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 72 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 161 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS A 456 GLN A 653 ASN A 668 HIS A 676 HIS B 72 ASN B 77 ASN B 179 HIS C 136 ASN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS D 183 ASN Y 18 ASN Y 226 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18071 Z= 0.244 Angle : 0.619 8.536 24656 Z= 0.316 Chirality : 0.044 0.278 2714 Planarity : 0.005 0.050 3007 Dihedral : 16.371 173.653 3146 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.22 % Allowed : 9.42 % Favored : 88.36 % 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: -3.63 (0.16), residues: 2018 helix: -2.67 (0.15), residues: 730 sheet: -1.83 (0.29), residues: 280 loop : -2.31 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 227 HIS 0.005 0.001 HIS C 111 PHE 0.023 0.002 PHE A 147 TYR 0.018 0.002 TYR A 265 ARG 0.006 0.001 ARG C 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 238 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7961 (tm130) cc_final: 0.7694 (tm-30) REVERT: A 91 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8707 (tp) REVERT: A 545 MET cc_start: 0.8062 (tpp) cc_final: 0.7753 (tpp) REVERT: A 571 LEU cc_start: 0.7698 (mm) cc_final: 0.7371 (mt) REVERT: B 152 MET cc_start: 0.6313 (mtm) cc_final: 0.5842 (ttm) REVERT: C 64 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7264 (mt-10) REVERT: D 21 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8245 (tp) REVERT: D 64 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7553 (mt-10) REVERT: D 103 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7949 (ttm170) REVERT: D 133 LYS cc_start: 0.7364 (mppt) cc_final: 0.6928 (mtpp) REVERT: E 145 PHE cc_start: 0.8980 (m-80) cc_final: 0.8649 (m-80) REVERT: E 244 MET cc_start: 0.8057 (mtp) cc_final: 0.7608 (mtm) REVERT: E 255 ASN cc_start: 0.8204 (t0) cc_final: 0.7564 (t0) REVERT: Y 101 LYS cc_start: 0.4005 (mtpp) cc_final: 0.3778 (mtpt) outliers start: 37 outliers final: 19 residues processed: 262 average time/residue: 0.3740 time to fit residues: 139.3107 Evaluate side-chains 223 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 201 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 18071 Z= 0.439 Angle : 0.689 8.886 24656 Z= 0.349 Chirality : 0.048 0.220 2714 Planarity : 0.006 0.064 3007 Dihedral : 16.321 173.735 3146 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.12 % Allowed : 10.98 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.17), residues: 2018 helix: -1.87 (0.17), residues: 750 sheet: -1.59 (0.29), residues: 282 loop : -2.15 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 674 HIS 0.008 0.001 HIS C 111 PHE 0.026 0.002 PHE E 15 TYR 0.017 0.002 TYR A 265 ARG 0.008 0.001 ARG E 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 203 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8127 (tm130) cc_final: 0.7863 (tm-30) REVERT: A 91 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8701 (tp) REVERT: A 545 MET cc_start: 0.8289 (tpp) cc_final: 0.7731 (tpp) REVERT: A 571 LEU cc_start: 0.7769 (mm) cc_final: 0.7388 (mt) REVERT: C 185 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8076 (ptt-90) REVERT: C 195 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7192 (tp30) REVERT: D 21 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8317 (tp) REVERT: D 64 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7651 (mt-10) REVERT: D 103 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8151 (ttm170) REVERT: D 133 LYS cc_start: 0.7333 (mppt) cc_final: 0.6923 (mtpp) REVERT: E 228 ARG cc_start: 0.7484 (ttm110) cc_final: 0.7276 (ttm170) REVERT: E 244 MET cc_start: 0.8091 (mtp) cc_final: 0.7691 (mtm) REVERT: E 255 ASN cc_start: 0.8385 (t0) cc_final: 0.7669 (t0) REVERT: Y 101 LYS cc_start: 0.4169 (mtpp) cc_final: 0.3915 (mtpt) outliers start: 52 outliers final: 35 residues processed: 237 average time/residue: 0.3538 time to fit residues: 120.9342 Evaluate side-chains 222 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 182 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain Y residue 215 LYS Chi-restraints excluded: chain Y residue 391 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 0.0040 chunk 121 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 77 optimal weight: 40.0000 chunk 108 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN A 456 GLN C 179 ASN E 38 GLN Y 254 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18071 Z= 0.156 Angle : 0.527 8.049 24656 Z= 0.269 Chirality : 0.041 0.177 2714 Planarity : 0.004 0.066 3007 Dihedral : 15.944 173.471 3146 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.46 % Allowed : 12.97 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.18), residues: 2018 helix: -1.03 (0.19), residues: 745 sheet: -1.32 (0.30), residues: 265 loop : -1.87 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 393 HIS 0.004 0.001 HIS Y 226 PHE 0.014 0.001 PHE E 159 TYR 0.012 0.001 TYR A 684 ARG 0.005 0.000 ARG E 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 193 time to evaluate : 2.258 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8123 (tm130) cc_final: 0.7797 (tm-30) REVERT: A 545 MET cc_start: 0.7986 (tpp) cc_final: 0.7686 (tpp) REVERT: A 572 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.6273 (ppp80) REVERT: B 152 MET cc_start: 0.6348 (mtm) cc_final: 0.5853 (ttm) REVERT: C 64 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7383 (mt-10) REVERT: C 66 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8597 (tt) REVERT: C 195 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7159 (tp30) REVERT: D 1 MET cc_start: 0.6561 (ttp) cc_final: 0.6312 (ttt) REVERT: D 133 LYS cc_start: 0.7412 (mppt) cc_final: 0.6900 (mtpp) REVERT: E 244 MET cc_start: 0.7963 (mtp) cc_final: 0.7569 (mtm) REVERT: E 255 ASN cc_start: 0.8357 (t0) cc_final: 0.7642 (t0) REVERT: Y 221 HIS cc_start: 0.6061 (m-70) cc_final: 0.5828 (m170) REVERT: Y 254 HIS cc_start: 0.6458 (OUTLIER) cc_final: 0.6209 (p90) outliers start: 41 outliers final: 22 residues processed: 220 average time/residue: 0.3436 time to fit residues: 109.9374 Evaluate side-chains 210 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG 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 Y residue 3 GLU Chi-restraints excluded: chain Y residue 254 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 chunk 154 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18071 Z= 0.233 Angle : 0.545 6.591 24656 Z= 0.278 Chirality : 0.042 0.171 2714 Planarity : 0.005 0.073 3007 Dihedral : 15.885 174.271 3146 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.10 % Allowed : 13.45 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.18), residues: 2018 helix: -0.65 (0.19), residues: 747 sheet: -1.24 (0.31), residues: 256 loop : -1.80 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 674 HIS 0.007 0.001 HIS Y 254 PHE 0.018 0.001 PHE D 276 TYR 0.012 0.001 TYR Y 297 ARG 0.010 0.000 ARG Y 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 1.894 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8170 (tm130) cc_final: 0.7862 (tm-30) REVERT: A 156 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7104 (tm-30) REVERT: A 545 MET cc_start: 0.8076 (tpp) cc_final: 0.7673 (tpp) REVERT: A 572 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6310 (ppp80) REVERT: B 152 MET cc_start: 0.6379 (mtm) cc_final: 0.5865 (ttm) REVERT: C 66 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8595 (tt) REVERT: C 195 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7181 (tp30) REVERT: D 1 MET cc_start: 0.6699 (ttp) cc_final: 0.6441 (ttt) REVERT: D 21 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8171 (tp) REVERT: D 64 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7640 (mt-10) REVERT: D 133 LYS cc_start: 0.7418 (mppt) cc_final: 0.6824 (mtpp) REVERT: E 244 MET cc_start: 0.8008 (mtp) cc_final: 0.7621 (mtm) REVERT: E 255 ASN cc_start: 0.8387 (t0) cc_final: 0.7625 (t0) REVERT: Y 101 LYS cc_start: 0.4324 (mtpp) cc_final: 0.4106 (mtpt) outliers start: 35 outliers final: 24 residues processed: 225 average time/residue: 0.3450 time to fit residues: 114.0852 Evaluate side-chains 213 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG 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 Y residue 3 GLU Chi-restraints excluded: chain Y residue 250 ASP Chi-restraints excluded: chain Y residue 301 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 56 optimal weight: 0.0870 chunk 90 optimal weight: 0.2980 chunk 166 optimal weight: 2.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN C 179 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18071 Z= 0.286 Angle : 0.571 8.744 24656 Z= 0.290 Chirality : 0.043 0.168 2714 Planarity : 0.005 0.067 3007 Dihedral : 15.888 174.156 3146 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.76 % Allowed : 13.33 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.18), residues: 2018 helix: -0.45 (0.20), residues: 743 sheet: -1.14 (0.31), residues: 262 loop : -1.73 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 239 HIS 0.006 0.001 HIS A 61 PHE 0.020 0.002 PHE A 59 TYR 0.014 0.001 TYR Y 297 ARG 0.010 0.001 ARG Y 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 191 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8167 (tm130) cc_final: 0.7876 (tm-30) REVERT: A 545 MET cc_start: 0.8163 (tpp) cc_final: 0.7712 (tpp) REVERT: A 572 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6394 (ppp80) REVERT: C 66 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8650 (tt) REVERT: C 195 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7201 (tp30) REVERT: D 1 MET cc_start: 0.6577 (ttp) cc_final: 0.6314 (ttt) REVERT: D 21 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8167 (tp) REVERT: D 64 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7669 (mt-10) REVERT: E 244 MET cc_start: 0.8035 (mtp) cc_final: 0.7643 (mtm) outliers start: 46 outliers final: 35 residues processed: 222 average time/residue: 0.3226 time to fit residues: 107.0689 Evaluate side-chains 219 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG 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 214 THR Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 301 MET Chi-restraints excluded: chain Y residue 391 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 144 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN C 179 ASN Y 328 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18071 Z= 0.173 Angle : 0.516 8.357 24656 Z= 0.264 Chirality : 0.042 0.199 2714 Planarity : 0.004 0.075 3007 Dihedral : 15.811 174.019 3146 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.10 % Allowed : 14.95 % Favored : 82.95 % 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: -1.58 (0.18), residues: 2018 helix: -0.18 (0.20), residues: 750 sheet: -1.09 (0.31), residues: 263 loop : -1.70 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 131 HIS 0.004 0.001 HIS A 61 PHE 0.020 0.001 PHE D 276 TYR 0.010 0.001 TYR Y 297 ARG 0.007 0.000 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 182 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8176 (tm130) cc_final: 0.7867 (tm-30) REVERT: A 545 MET cc_start: 0.8045 (tpp) cc_final: 0.7676 (tpp) REVERT: A 572 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6369 (ppp80) REVERT: C 66 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8583 (tt) REVERT: C 195 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7189 (tp30) REVERT: D 1 MET cc_start: 0.6379 (ttp) cc_final: 0.6114 (ttt) REVERT: D 21 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8068 (tp) REVERT: D 64 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7657 (mt-10) REVERT: D 195 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: E 244 MET cc_start: 0.7954 (mtp) cc_final: 0.7373 (mtm) REVERT: Y 101 LYS cc_start: 0.4433 (mtpp) cc_final: 0.4201 (mtpt) outliers start: 35 outliers final: 25 residues processed: 205 average time/residue: 0.3386 time to fit residues: 101.8077 Evaluate side-chains 205 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG 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 214 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 301 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.0770 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 134 optimal weight: 0.0870 chunk 156 optimal weight: 0.6980 chunk 164 optimal weight: 0.6980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN Y 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18071 Z= 0.161 Angle : 0.506 7.951 24656 Z= 0.257 Chirality : 0.041 0.210 2714 Planarity : 0.004 0.064 3007 Dihedral : 15.738 174.395 3146 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.46 % Allowed : 14.89 % Favored : 82.65 % 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: -1.31 (0.19), residues: 2018 helix: 0.11 (0.20), residues: 747 sheet: -0.93 (0.31), residues: 265 loop : -1.60 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 131 HIS 0.006 0.001 HIS A 61 PHE 0.014 0.001 PHE E 159 TYR 0.009 0.001 TYR Y 297 ARG 0.006 0.000 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8223 (tm130) cc_final: 0.7896 (tm-30) REVERT: A 26 TYR cc_start: 0.7425 (m-80) cc_final: 0.7200 (m-80) REVERT: A 29 ASP cc_start: 0.6871 (t0) cc_final: 0.6479 (m-30) REVERT: A 545 MET cc_start: 0.8008 (tpp) cc_final: 0.7684 (tpp) REVERT: A 572 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6350 (ppp80) REVERT: A 773 MET cc_start: 0.5628 (mtt) cc_final: 0.5310 (mtp) REVERT: B 152 MET cc_start: 0.6248 (mtm) cc_final: 0.5832 (ttm) REVERT: C 66 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8599 (tt) REVERT: C 191 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7751 (mt-10) REVERT: C 195 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7199 (tp30) REVERT: D 1 MET cc_start: 0.6314 (ttp) cc_final: 0.6021 (ttt) REVERT: D 21 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8036 (tp) REVERT: D 195 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: E 244 MET cc_start: 0.7928 (mtp) cc_final: 0.7547 (mtm) REVERT: Y 3 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: Y 101 LYS cc_start: 0.4419 (mtpp) cc_final: 0.4176 (mtpt) REVERT: Y 221 HIS cc_start: 0.6180 (m-70) cc_final: 0.5918 (m170) REVERT: Y 390 PRO cc_start: 0.3823 (Cg_exo) cc_final: 0.3596 (Cg_endo) outliers start: 41 outliers final: 31 residues processed: 212 average time/residue: 0.3375 time to fit residues: 106.0934 Evaluate side-chains 217 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG 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 214 THR Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 301 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 169 optimal weight: 0.0980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN E 200 HIS Y 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 0.036 18071 Z= 0.164 Angle : 0.507 8.532 24656 Z= 0.258 Chirality : 0.041 0.219 2714 Planarity : 0.004 0.078 3007 Dihedral : 15.699 174.622 3146 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.52 % Allowed : 14.83 % Favored : 82.65 % 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: -1.21 (0.19), residues: 2018 helix: 0.19 (0.20), residues: 756 sheet: -0.78 (0.32), residues: 261 loop : -1.60 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 131 HIS 0.006 0.001 HIS A 61 PHE 0.021 0.001 PHE D 276 TYR 0.009 0.001 TYR Y 297 ARG 0.007 0.000 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8224 (tm130) cc_final: 0.7903 (tm-30) REVERT: A 26 TYR cc_start: 0.7407 (m-80) cc_final: 0.7192 (m-80) REVERT: A 29 ASP cc_start: 0.6724 (t0) cc_final: 0.6318 (m-30) REVERT: A 545 MET cc_start: 0.8074 (tpp) cc_final: 0.7765 (tpp) REVERT: A 572 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6325 (ppp80) REVERT: A 773 MET cc_start: 0.5606 (mtt) cc_final: 0.5301 (mtp) REVERT: B 178 TYR cc_start: 0.7248 (m-80) cc_final: 0.6965 (m-80) REVERT: C 66 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8624 (tt) REVERT: C 191 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7708 (mt-10) REVERT: C 195 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7221 (tp30) REVERT: D 1 MET cc_start: 0.6364 (ttp) cc_final: 0.6042 (ttt) REVERT: D 21 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8091 (tp) REVERT: E 244 MET cc_start: 0.7928 (mtp) cc_final: 0.7551 (mtm) REVERT: Y 3 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: Y 101 LYS cc_start: 0.4391 (mtpp) cc_final: 0.4162 (mtpt) REVERT: Y 221 HIS cc_start: 0.6275 (m-70) cc_final: 0.6019 (m170) outliers start: 42 outliers final: 33 residues processed: 213 average time/residue: 0.3371 time to fit residues: 105.1790 Evaluate side-chains 212 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 174 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG 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 214 THR Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 301 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 177 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN E 200 HIS Y 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18071 Z= 0.188 Angle : 0.518 11.920 24656 Z= 0.263 Chirality : 0.042 0.261 2714 Planarity : 0.004 0.061 3007 Dihedral : 15.714 174.778 3146 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.80 % Rotamer: Outliers : 2.52 % Allowed : 14.71 % Favored : 82.77 % 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: -1.17 (0.19), residues: 2018 helix: 0.24 (0.20), residues: 761 sheet: -0.75 (0.32), residues: 259 loop : -1.59 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 131 HIS 0.013 0.001 HIS A 60 PHE 0.021 0.001 PHE D 276 TYR 0.009 0.001 TYR Y 297 ARG 0.007 0.000 ARG D 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8236 (tm130) cc_final: 0.7929 (tm-30) REVERT: A 29 ASP cc_start: 0.6702 (t0) cc_final: 0.6282 (m-30) REVERT: A 545 MET cc_start: 0.8111 (tpp) cc_final: 0.7788 (tpp) REVERT: A 572 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6366 (ppp80) REVERT: A 773 MET cc_start: 0.5581 (mtt) cc_final: 0.5303 (mtp) REVERT: C 66 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8625 (tt) REVERT: C 191 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7716 (mt-10) REVERT: C 195 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7223 (tp30) REVERT: D 1 MET cc_start: 0.6389 (ttp) cc_final: 0.6063 (ttt) REVERT: D 21 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8091 (tp) REVERT: E 244 MET cc_start: 0.7946 (mtp) cc_final: 0.7569 (mtm) REVERT: Y 3 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6482 (mp0) REVERT: Y 101 LYS cc_start: 0.4350 (mtpp) cc_final: 0.4111 (mtpt) REVERT: Y 221 HIS cc_start: 0.6258 (m-70) cc_final: 0.6007 (m170) outliers start: 42 outliers final: 32 residues processed: 204 average time/residue: 0.3383 time to fit residues: 101.2375 Evaluate side-chains 204 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 167 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG 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 214 THR Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 301 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN E 200 HIS Y 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.183024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135583 restraints weight = 23160.583| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.55 r_work: 0.3164 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18071 Z= 0.175 Angle : 0.512 12.378 24656 Z= 0.261 Chirality : 0.041 0.245 2714 Planarity : 0.004 0.076 3007 Dihedral : 15.695 174.787 3146 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 2.46 % Allowed : 14.89 % Favored : 82.65 % 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 (0.19), residues: 2018 helix: 0.33 (0.20), residues: 761 sheet: -0.73 (0.32), residues: 259 loop : -1.57 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 131 HIS 0.007 0.001 HIS A 60 PHE 0.015 0.001 PHE E 159 TYR 0.030 0.001 TYR A 26 ARG 0.007 0.000 ARG E 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3750.81 seconds wall clock time: 68 minutes 53.29 seconds (4133.29 seconds total)