Starting phenix.real_space_refine (version: dev) on Wed Mar 15 06:13:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/03_2023/6upk_20840.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/03_2023/6upk_20840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/03_2023/6upk_20840.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/03_2023/6upk_20840.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/03_2023/6upk_20840.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/03_2023/6upk_20840.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.025 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 Process input model Symmetric amino acids flipped Residue "D ARG 31": "NH1" <-> "NH2" Residue "G ARG 525": "NH1" <-> "NH2" Residue "G ARG 581": "NH1" <-> "NH2" Residue "G ARG 623": "NH1" <-> "NH2" Residue "G ARG 631": "NH1" <-> "NH2" Residue "G ARG 657": "NH1" <-> "NH2" Residue "G ARG 812": "NH1" <-> "NH2" Residue "H PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H ARG 211": "NH1" <-> "NH2" Residue "H ARG 241": "NH1" <-> "NH2" Residue "H ARG 297": "NH1" <-> "NH2" Residue "H ARG 324": "NH1" <-> "NH2" Residue "H ARG 357": "NH1" <-> "NH2" Residue "H ARG 387": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 13861 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3331 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 403} Chain breaks: 4 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'UNK:plan-1': 41} Unresolved non-hydrogen planarities: 41 Chain: "H" Number of atoms: 3326 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 411, 3314 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 11, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 411, 3314 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 11, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 3374 Chain: "I" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1466 Classifications: {'DNA': 72} Link IDs: {'rna3p': 71} Chain: "J" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1486 Classifications: {'DNA': 72} Link IDs: {'rna3p': 71} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER H 86 " occ=0.66 ... (10 atoms not shown) pdb=" OG BSER H 86 " occ=0.34 residue: pdb=" N ACYS H 207 " occ=0.61 ... (10 atoms not shown) pdb=" SG BCYS H 207 " occ=0.39 Time building chain proxies: 9.73, per 1000 atoms: 0.70 Number of scatterers: 13861 At special positions: 0 Unit cell: (95.4045, 120.659, 165.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 144 15.00 O 2827 8.00 N 2497 7.00 C 8349 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.90 Conformation dependent library (CDL) restraints added in 2.2 seconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 16 sheets defined 39.6% alpha, 17.8% beta 65 base pairs and 102 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.921A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.872A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.650A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 48 through 77 removed outlier: 4.211A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.970A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.557A pdb=" N LYS C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.137A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 87 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.763A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D 69 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.756A pdb=" N ALA D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 57 removed outlier: 4.205A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 79 removed outlier: 4.191A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 115 removed outlier: 3.925A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU E 103 " --> pdb=" O TYR E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 removed outlier: 4.655A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.940A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.244A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.685A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 636 removed outlier: 4.396A pdb=" N ILE G 624 " --> pdb=" O ASN G 620 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE G 625 " --> pdb=" O ALA G 621 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS G 626 " --> pdb=" O PHE G 622 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU G 627 " --> pdb=" O ARG G 623 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL G 628 " --> pdb=" O ILE G 624 " (cutoff:3.500A) Processing helix chain 'G' and resid 763 through 788 removed outlier: 3.635A pdb=" N GLN G 767 " --> pdb=" O LEU G 763 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS G 775 " --> pdb=" O GLU G 771 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU G 776 " --> pdb=" O MET G 772 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA G 779 " --> pdb=" O LYS G 775 " (cutoff:3.500A) Processing helix chain 'G' and resid 878 through 890 Processing helix chain 'G' and resid 901 through 910 Processing helix chain 'G' and resid 916 through 924 removed outlier: 3.717A pdb=" N GLY G 920 " --> pdb=" O PHE G 917 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLY G 921 " --> pdb=" O GLU G 918 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TRP G 922 " --> pdb=" O GLN G 919 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 90 removed outlier: 4.258A pdb=" N ASER H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 180 removed outlier: 3.549A pdb=" N UNK H 180 " --> pdb=" O UNK H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 299 Processing helix chain 'H' and resid 309 through 323 removed outlier: 3.796A pdb=" N SER H 315 " --> pdb=" O TYR H 311 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL H 317 " --> pdb=" O MET H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 338 Processing helix chain 'H' and resid 407 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.269A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.917A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 530 through 532 removed outlier: 3.722A pdb=" N TYR G 530 " --> pdb=" O ILE G 539 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 554 through 562 removed outlier: 6.642A pdb=" N GLU G 597 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL H 163 " --> pdb=" O GLU G 597 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR G 599 " --> pdb=" O MET H 161 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL H 163 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR H 140 " --> pdb=" O THR H 147 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN H 138 " --> pdb=" O GLU H 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 698 through 700 removed outlier: 3.585A pdb=" N GLY G 686 " --> pdb=" O HIS G 683 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU G 665 " --> pdb=" O GLY G 678 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU G 680 " --> pdb=" O LYS G 663 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS G 663 " --> pdb=" O LEU G 680 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA G 682 " --> pdb=" O LYS G 661 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS G 661 " --> pdb=" O ALA G 682 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ASP G 664 " --> pdb=" O GLU G 743 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU G 743 " --> pdb=" O ASP G 664 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ARG G 734 " --> pdb=" O ASN G 726 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ASN G 726 " --> pdb=" O ARG G 734 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR G 736 " --> pdb=" O LEU G 724 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL G 738 " --> pdb=" O PHE G 722 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL G 719 " --> pdb=" O PHE G 709 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE G 709 " --> pdb=" O VAL G 719 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS G 721 " --> pdb=" O ALA G 707 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA G 707 " --> pdb=" O HIS G 721 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS G 723 " --> pdb=" O LYS G 705 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 806 through 808 removed outlier: 3.501A pdb=" N PHE G 833 " --> pdb=" O ASN G 826 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 870 through 874 removed outlier: 6.770A pdb=" N MET G 870 " --> pdb=" O ILE G 859 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE G 859 " --> pdb=" O MET G 870 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ASN G 872 " --> pdb=" O MET G 857 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET G 857 " --> pdb=" O ASN G 872 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N THR G 894 " --> pdb=" O GLU G 841 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE G 843 " --> pdb=" O THR G 894 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.597A pdb=" N ASP H 75 " --> pdb=" O TYR H 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU H 62 " --> pdb=" O TYR H 74 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS H 63 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE H 52 " --> pdb=" O LYS H 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 111 through 114 removed outlier: 4.698A pdb=" N LEU H 119 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU H 130 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE H 121 " --> pdb=" O VAL H 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 200 through 201 removed outlier: 3.676A pdb=" N CYS H 200 " --> pdb=" O ILE H 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 200 through 201 removed outlier: 3.676A pdb=" N CYS H 200 " --> pdb=" O ILE H 218 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 239 through 246 removed outlier: 6.507A pdb=" N SER H 258 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU H 242 " --> pdb=" O VAL H 256 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL H 256 " --> pdb=" O LEU H 242 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU H 244 " --> pdb=" O PHE H 254 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE H 254 " --> pdb=" O LEU H 244 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLN H 252 " --> pdb=" O PRO H 246 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N HIS H 271 " --> pdb=" O LEU H 259 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N ARG H 269 " --> pdb=" O PRO H 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 342 through 344 Processing sheet with id=AB7, first strand: chain 'H' and resid 400 through 406 removed outlier: 6.520A pdb=" N PHE H 389 " --> pdb=" O SER H 405 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LYS H 426 " --> pdb=" O SER H 375 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL H 377 " --> pdb=" O LYS H 426 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 152 hydrogen bonds 244 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 102 stacking parallelities Total time for adding SS restraints: 6.08 Time building geometry restraints manager: 7.20 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: 3386 1.33 - 1.45: 3635 1.45 - 1.57: 7041 1.57 - 1.70: 286 1.70 - 1.82: 73 Bond restraints: 14421 Sorted by residual: bond pdb=" CA GLU H 299 " pdb=" C GLU H 299 " ideal model delta sigma weight residual 1.523 1.558 -0.034 1.34e-02 5.57e+03 6.56e+00 bond pdb=" N ASP H 101 " pdb=" CA ASP H 101 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.58e+00 bond pdb=" C TYR H 93 " pdb=" N ARG H 94 " ideal model delta sigma weight residual 1.333 1.306 0.028 1.43e-02 4.89e+03 3.74e+00 bond pdb=" C LYS H 100 " pdb=" N ASP H 101 " ideal model delta sigma weight residual 1.329 1.354 -0.025 1.40e-02 5.10e+03 3.29e+00 bond pdb=" N GLU H 299 " pdb=" CA GLU H 299 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.13e+00 ... (remaining 14416 not shown) Histogram of bond angle deviations from ideal: 98.05 - 105.24: 749 105.24 - 112.43: 7552 112.43 - 119.62: 4677 119.62 - 126.81: 6616 126.81 - 134.01: 482 Bond angle restraints: 20076 Sorted by residual: angle pdb=" N TYR H 93 " pdb=" CA TYR H 93 " pdb=" C TYR H 93 " ideal model delta sigma weight residual 111.75 122.51 -10.76 1.28e+00 6.10e-01 7.07e+01 angle pdb=" N ILE G 586 " pdb=" CA ILE G 586 " pdb=" C ILE G 586 " ideal model delta sigma weight residual 111.91 105.33 6.58 8.90e-01 1.26e+00 5.46e+01 angle pdb=" N THR H 170 " pdb=" CA THR H 170 " pdb=" C THR H 170 " ideal model delta sigma weight residual 111.28 102.21 9.07 1.35e+00 5.49e-01 4.51e+01 angle pdb=" N TYR E 41 " pdb=" CA TYR E 41 " pdb=" C TYR E 41 " ideal model delta sigma weight residual 110.50 119.93 -9.43 1.41e+00 5.03e-01 4.47e+01 angle pdb=" N ARG E 40 " pdb=" CA ARG E 40 " pdb=" C ARG E 40 " ideal model delta sigma weight residual 110.23 103.07 7.16 1.45e+00 4.76e-01 2.44e+01 ... (remaining 20071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.34: 7319 27.34 - 54.68: 721 54.68 - 82.01: 148 82.01 - 109.35: 3 109.35 - 136.69: 2 Dihedral angle restraints: 8193 sinusoidal: 4207 harmonic: 3986 Sorted by residual: dihedral pdb=" CA PHE H 165 " pdb=" C PHE H 165 " pdb=" N TYR H 166 " pdb=" CA TYR H 166 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA TYR H 11 " pdb=" C TYR H 11 " pdb=" N GLN H 12 " pdb=" CA GLN H 12 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PHE H 89 " pdb=" C PHE H 89 " pdb=" N LYS H 90 " pdb=" CA LYS H 90 " ideal model delta harmonic sigma weight residual -180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 8190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2085 0.097 - 0.193: 152 0.193 - 0.290: 8 0.290 - 0.386: 2 0.386 - 0.482: 2 Chirality restraints: 2249 Sorted by residual: chirality pdb=" CB VAL H 362 " pdb=" CA VAL H 362 " pdb=" CG1 VAL H 362 " pdb=" CG2 VAL H 362 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" CA TYR H 93 " pdb=" N TYR H 93 " pdb=" C TYR H 93 " pdb=" CB TYR H 93 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB ILE G 718 " pdb=" CA ILE G 718 " pdb=" CG1 ILE G 718 " pdb=" CG2 ILE G 718 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 2246 not shown) Planarity restraints: 2064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 167 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C VAL H 167 " 0.070 2.00e-02 2.50e+03 pdb=" O VAL H 167 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO H 168 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 92 " -0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C HIS H 92 " 0.064 2.00e-02 2.50e+03 pdb=" O HIS H 92 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR H 93 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 40 " -0.023 2.00e-02 2.50e+03 1.88e-02 7.10e+00 pdb=" CG TYR D 40 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR D 40 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D 40 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 40 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 40 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 40 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 40 " -0.000 2.00e-02 2.50e+03 ... (remaining 2061 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 27 2.24 - 2.90: 5238 2.90 - 3.57: 21762 3.57 - 4.23: 36645 4.23 - 4.90: 54899 Nonbonded interactions: 118571 Sorted by model distance: nonbonded pdb=" NZ LYS G 626 " pdb=" OP1 DT I -6 " model vdw 1.570 2.520 nonbonded pdb=" NE2 GLN H 267 " pdb=" OP1 DC J 1 " model vdw 1.571 2.520 nonbonded pdb=" CG GLN H 267 " pdb=" OP1 DC J 1 " model vdw 1.687 3.440 nonbonded pdb=" NH1 ARG E 40 " pdb=" N2 DG J -8 " model vdw 1.734 3.200 nonbonded pdb=" CD GLN H 267 " pdb=" OP1 DC J 1 " model vdw 1.833 3.270 ... (remaining 118566 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 'B' selection = (chain 'F' and resid 25 through 102) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 144 5.49 5 S 44 5.16 5 C 8349 2.51 5 N 2497 2.21 5 O 2827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.32 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.280 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: 3.020 Check model and map are aligned: 0.200 Process input model: 45.440 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 0.076 14421 Z= 0.343 Angle : 0.938 10.763 20076 Z= 0.552 Chirality : 0.053 0.482 2249 Planarity : 0.007 0.064 2064 Dihedral : 20.345 136.691 5617 Min Nonbonded Distance : 1.570 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -3.94 (0.19), residues: 1292 helix: -2.50 (0.17), residues: 446 sheet: -3.00 (0.34), residues: 169 loop : -2.58 (0.20), residues: 677 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3317 time to fit residues: 62.7955 Evaluate side-chains 85 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.512 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN B 64 ASN C 68 ASN C 110 ASN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 25 ASN G 585 ASN G 604 ASN G 619 GLN ** G 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 739 GLN H 12 GLN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 ASN ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 ASN ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 14421 Z= 0.339 Angle : 0.762 10.821 20076 Z= 0.425 Chirality : 0.043 0.205 2249 Planarity : 0.006 0.062 2064 Dihedral : 26.441 143.782 2951 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 34.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -2.83 (0.21), residues: 1292 helix: -1.07 (0.21), residues: 470 sheet: -2.64 (0.38), residues: 150 loop : -2.31 (0.22), residues: 672 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 112 average time/residue: 0.3175 time to fit residues: 50.4597 Evaluate side-chains 81 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 1.487 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1368 time to fit residues: 2.9757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 40.0000 chunk 36 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 710 GLN G 723 HIS ** G 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 739 GLN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 14421 Z= 0.305 Angle : 0.713 10.521 20076 Z= 0.401 Chirality : 0.042 0.226 2249 Planarity : 0.005 0.067 2064 Dihedral : 27.006 141.471 2951 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 35.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.42 (0.22), residues: 1292 helix: -0.53 (0.22), residues: 474 sheet: -2.58 (0.36), residues: 162 loop : -2.17 (0.23), residues: 656 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 103 average time/residue: 0.3005 time to fit residues: 44.4168 Evaluate side-chains 71 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1339 time to fit residues: 2.7802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 89 optimal weight: 50.0000 chunk 134 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 739 GLN ** G 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 14421 Z= 0.267 Angle : 0.659 10.585 20076 Z= 0.370 Chirality : 0.041 0.204 2249 Planarity : 0.005 0.065 2064 Dihedral : 27.283 142.799 2951 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 32.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -2.09 (0.22), residues: 1292 helix: -0.13 (0.22), residues: 478 sheet: -2.39 (0.37), residues: 164 loop : -2.10 (0.23), residues: 650 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 105 average time/residue: 0.2808 time to fit residues: 42.4051 Evaluate side-chains 73 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1234 time to fit residues: 2.2331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 3.9990 chunk 80 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 72 optimal weight: 50.0000 chunk 127 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: