Starting phenix.real_space_refine (version: dev) on Thu Dec 15 23:41:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/12_2022/6wu9_21907.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/12_2022/6wu9_21907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/12_2022/6wu9_21907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/12_2022/6wu9_21907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/12_2022/6wu9_21907.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/12_2022/6wu9_21907.pdb" } resolution = 2.9 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= -0.000 sd= 0.009 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "F ASP 153": "OD1" <-> "OD2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "L GLU 5": "OE1" <-> "OE2" Residue "L GLU 56": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 119": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "T ARG 16": "NH1" <-> "NH2" Residue "U PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 80": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 82295 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 58793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2739, 58793 Classifications: {'RNA': 2739} Modifications used: {'rna2p_pur': 287, 'rna2p_pyr': 144, 'rna3p_pur': 1306, 'rna3p_pyr': 1002} Link IDs: {'rna2p': 431, 'rna3p': 2307} Chain breaks: 5 Chain: "B" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2480 Classifications: {'RNA': 116} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 48} Link IDs: {'rna2p': 12, 'rna3p': 103} Chain: "D" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1579 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "E" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1574 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain: "F" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1392 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "G" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1345 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "K" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1130 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 7, 'TRANS': 137} Chain: "L" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 922 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "M" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1095 Classifications: {'peptide': 146} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 140} Chain: "N" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1118 Classifications: {'peptide': 141} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 133} Chain: "O" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 991 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "P" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 899 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 924 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "R" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'TRANS': 117} Chain: "S" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 784 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "T" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 849 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "U" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 720 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "V" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "X" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 572 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "Y" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 425 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "Z" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 504 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "0" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 435 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "2" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "3" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 419 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "4" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "5" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 522 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "6" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 304 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" 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 80472 SG CYS 2 30 183.480 140.306 86.693 1.00 11.93 S ATOM 80492 SG CYS 2 33 185.981 137.507 88.840 1.00 15.95 S ATOM 80570 SG CYS 2 43 182.310 138.566 90.028 1.00 7.68 S ATOM 80588 SG CYS 2 46 185.390 140.813 90.534 1.00 11.63 S ATOM 80745 SG CYS 3 9 71.872 42.693 136.022 1.00 17.23 S ATOM 80764 SG CYS 3 12 75.568 41.685 137.123 1.00 19.37 S ATOM 80977 SG CYS 3 36 74.555 40.855 133.529 1.00 12.53 S ATOM 82073 SG CYS 6 11 73.835 124.568 49.335 1.00 16.19 S ATOM 82098 SG CYS 6 14 77.324 122.889 50.457 1.00 14.26 S ATOM 82204 SG CYS 6 27 77.133 126.153 48.919 1.00 10.76 S Time building chain proxies: 34.94, per 1000 atoms: 0.42 Number of scatterers: 82295 At special positions: 0 Unit cell: (220.497, 209.527, 225.982, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 71 16.00 P 2855 15.00 O 23604 8.00 N 15251 7.00 C 40511 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: 32.29 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 101 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 33 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 43 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 46 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 30 " pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 9 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 12 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 36 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" ND1 HIS 6 33 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 27 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 14 " Number of angles added : 9 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4930 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 40 sheets defined 28.4% alpha, 20.2% beta 928 base pairs and 1531 stacking pairs defined. Time for finding SS restraints: 27.06 Creating SS restraints... Processing helix chain 'D' and resid 62 through 71 removed outlier: 4.319A pdb=" N LYS D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'E' and resid 29 through 43 removed outlier: 3.512A pdb=" N VAL E 33 " --> pdb=" O ASN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 119 Processing helix chain 'E' and resid 135 through 146 Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.722A pdb=" N VAL E 186 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 207 removed outlier: 3.592A pdb=" N VAL E 205 " --> pdb=" O GLN E 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 20 removed outlier: 6.122A pdb=" N THR F 13 " --> pdb=" O ILE F 9 " (cutoff:3.500A) Proline residue: F 14 - end of helix Processing helix chain 'F' and resid 49 through 61 Processing helix chain 'F' and resid 74 through 78 removed outlier: 3.662A pdb=" N PHE F 77 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 removed outlier: 3.682A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL F 106 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 162 through 172 removed outlier: 3.706A pdb=" N SER F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 81 removed outlier: 4.030A pdb=" N PHE G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 149 removed outlier: 3.840A pdb=" N VAL G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 38 Processing helix chain 'K' and resid 60 through 63 Processing helix chain 'K' and resid 68 through 73 Processing helix chain 'K' and resid 91 through 96 removed outlier: 3.866A pdb=" N ASP K 95 " --> pdb=" O GLY K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 108 removed outlier: 4.016A pdb=" N LEU K 101 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE K 102 " --> pdb=" O SER K 98 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 120 removed outlier: 3.570A pdb=" N LYS K 118 " --> pdb=" O THR K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 137 removed outlier: 3.643A pdb=" N GLN K 136 " --> pdb=" O HIS K 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 109 removed outlier: 4.451A pdb=" N GLU L 108 " --> pdb=" O ARG L 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 41 removed outlier: 3.602A pdb=" N ARG M 41 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.557A pdb=" N ARG M 60 " --> pdb=" O PRO M 56 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 56 through 61' Processing helix chain 'M' and resid 80 through 84 removed outlier: 3.671A pdb=" N ARG M 84 " --> pdb=" O THR M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 97 Processing helix chain 'M' and resid 129 through 140 Processing helix chain 'N' and resid 44 through 57 removed outlier: 3.755A pdb=" N TYR N 57 " --> pdb=" O ALA N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 123 removed outlier: 3.832A pdb=" N HIS N 123 " --> pdb=" O ARG N 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 removed outlier: 3.632A pdb=" N LYS O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU O 24 " --> pdb=" O ILE O 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE O 25 " --> pdb=" O THR O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 52 removed outlier: 3.636A pdb=" N LYS O 38 " --> pdb=" O GLU O 34 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU O 50 " --> pdb=" O LYS O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 Processing helix chain 'O' and resid 86 through 92 Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'P' and resid 6 through 19 removed outlier: 3.741A pdb=" N THR P 10 " --> pdb=" O ASP P 6 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG P 14 " --> pdb=" O THR P 10 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG P 17 " --> pdb=" O LYS P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 86 removed outlier: 4.029A pdb=" N ALA P 73 " --> pdb=" O THR P 69 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA P 74 " --> pdb=" O GLU P 70 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL P 75 " --> pdb=" O THR P 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 114 removed outlier: 3.707A pdb=" N ALA P 106 " --> pdb=" O GLY P 102 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU P 107 " --> pdb=" O ARG P 103 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN P 114 " --> pdb=" O ALA P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 11 removed outlier: 4.655A pdb=" N GLU Q 11 " --> pdb=" O GLU Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 56 removed outlier: 4.097A pdb=" N SER Q 56 " --> pdb=" O ALA Q 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 53 through 56' Processing helix chain 'Q' and resid 97 through 103 removed outlier: 3.675A pdb=" N ALA Q 102 " --> pdb=" O TYR Q 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 20 removed outlier: 3.747A pdb=" N LYS R 12 " --> pdb=" O THR R 8 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 Processing helix chain 'R' and resid 31 through 70 removed outlier: 3.913A pdb=" N ARG R 51 " --> pdb=" O PHE R 47 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 73 No H-bonds generated for 'chain 'R' and resid 71 through 73' Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 117 Processing helix chain 'T' and resid 18 through 27 removed outlier: 3.635A pdb=" N ARG T 23 " --> pdb=" O PRO T 19 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU T 24 " --> pdb=" O ARG T 20 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL T 25 " --> pdb=" O LYS T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 33 through 43 removed outlier: 3.645A pdb=" N ILE T 38 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER T 39 " --> pdb=" O ALA T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 66 removed outlier: 3.553A pdb=" N LYS T 54 " --> pdb=" O GLY T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 96 No H-bonds generated for 'chain 'T' and resid 94 through 96' Processing helix chain 'U' and resid 13 through 20 removed outlier: 3.870A pdb=" N LEU U 18 " --> pdb=" O GLU U 14 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA U 19 " --> pdb=" O LYS U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 47 Processing helix chain 'Y' and resid 51 through 55 Processing helix chain 'Z' and resid 3 through 7 Processing helix chain 'Z' and resid 10 through 34 removed outlier: 3.719A pdb=" N LEU Z 15 " --> pdb=" O THR Z 11 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA Z 33 " --> pdb=" O ARG Z 29 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR Z 34 " --> pdb=" O PHE Z 30 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 61 removed outlier: 3.706A pdb=" N GLU Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) Processing helix chain '0' and resid 16 through 27 Processing helix chain '0' and resid 40 through 51 removed outlier: 3.519A pdb=" N LYS 0 44 " --> pdb=" O ASN 0 40 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 17 Processing helix chain '2' and resid 18 through 20 No H-bonds generated for 'chain '2' and resid 18 through 20' Processing helix chain '4' and resid 8 through 17 removed outlier: 3.650A pdb=" N ARG 4 12 " --> pdb=" O ASN 4 8 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 17 through 23 Processing helix chain '4' and resid 24 through 36 removed outlier: 3.631A pdb=" N ARG 4 28 " --> pdb=" O THR 4 24 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG 4 29 " --> pdb=" O LYS 4 25 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 12 removed outlier: 3.637A pdb=" N LYS 5 12 " --> pdb=" O ARG 5 8 " (cutoff:3.500A) Processing helix chain '5' and resid 32 through 36 Processing helix chain '5' and resid 37 through 44 Processing helix chain '5' and resid 51 through 59 removed outlier: 3.570A pdb=" N ARG 5 57 " --> pdb=" O GLY 5 53 " (cutoff:3.500A) Processing helix chain '5' and resid 60 through 63 removed outlier: 3.873A pdb=" N ALA 5 63 " --> pdb=" O GLN 5 60 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 60 through 63' Processing helix chain '6' and resid 30 through 33 Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 16 removed outlier: 6.813A pdb=" N VAL D 27 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLN D 14 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE D 23 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS D 189 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL D 176 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLU D 175 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP D 106 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N THR D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU D 199 " --> pdb=" O THR D 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 77 through 84 removed outlier: 6.460A pdb=" N LYS D 77 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP D 55 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA D 48 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL D 38 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 116 through 120 removed outlier: 3.569A pdb=" N GLY D 118 " --> pdb=" O MET D 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 16 through 18 removed outlier: 10.091A pdb=" N ASN E 3 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N ALA E 125 " --> pdb=" O ASN E 3 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA E 5 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR E 195 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL E 155 " --> pdb=" O THR E 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 87 through 91 removed outlier: 3.640A pdb=" N ALA F 87 " --> pdb=" O MET F 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.881A pdb=" N LYS G 18 " --> pdb=" O THR G 25 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR G 25 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP G 20 " --> pdb=" O ASN G 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 83 through 87 removed outlier: 3.573A pdb=" N PHE G 83 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY G 135 " --> pdb=" O PHE G 83 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS G 134 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.525A pdb=" N ARG G 95 " --> pdb=" O ASN G 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 123 through 126 removed outlier: 6.620A pdb=" N VAL K 55 " --> pdb=" O ASN K 124 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR K 126 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL K 57 " --> pdb=" O TYR K 126 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP K 16 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 75 through 78 removed outlier: 7.039A pdb=" N TYR K 75 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL K 88 " --> pdb=" O TYR K 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 7 through 10 removed outlier: 6.251A pdb=" N ARG L 17 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA L 16 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA L 46 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU L 18 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA L 84 " --> pdb=" O ARG L 7 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG L 9 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE L 86 " --> pdb=" O ARG L 9 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 69 through 70 removed outlier: 6.928A pdb=" N THR Q 58 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG Q 50 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR Q 60 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL Q 64 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N GLU Q 44 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR Q 25 " --> pdb=" O VAL Q 87 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 110 through 111 Processing sheet with id=AB5, first strand: chain 'M' and resid 122 through 125 removed outlier: 3.675A pdb=" N ALA M 125 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 63 through 66 removed outlier: 6.873A pdb=" N LEU N 34 " --> pdb=" O MET N 103 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU N 105 " --> pdb=" O TRP N 32 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP N 32 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 40 through 43 Processing sheet with id=AB8, first strand: chain 'O' and resid 29 through 33 removed outlier: 6.585A pdb=" N MET O 120 " --> pdb=" O THR O 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 34 through 35 removed outlier: 6.994A pdb=" N ILE P 40 " --> pdb=" O SER P 57 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N SER P 57 " --> pdb=" O ILE P 40 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA P 42 " --> pdb=" O SER P 55 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER P 55 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL P 44 " --> pdb=" O LEU P 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 34 through 35 Processing sheet with id=AC2, first strand: chain 'Q' and resid 32 through 34 removed outlier: 3.636A pdb=" N ARG Q 37 " --> pdb=" O GLU Q 34 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 10 through 14 removed outlier: 3.564A pdb=" N ALA S 3 " --> pdb=" O VAL S 14 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE S 4 " --> pdb=" O ILE S 39 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL S 41 " --> pdb=" O LYS S 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 19 through 22 removed outlier: 6.682A pdb=" N TYR S 92 " --> pdb=" O HIS S 65 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N HIS S 65 " --> pdb=" O TYR S 92 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS S 94 " --> pdb=" O GLU S 63 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU S 59 " --> pdb=" O GLU S 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 71 through 76 Processing sheet with id=AC6, first strand: chain 'T' and resid 7 through 15 removed outlier: 5.611A pdb=" N LYS T 9 " --> pdb=" O VAL T 112 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL T 112 " --> pdb=" O LYS T 9 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR T 11 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL T 110 " --> pdb=" O THR T 11 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS T 13 " --> pdb=" O ILE T 108 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE T 108 " --> pdb=" O LYS T 13 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU T 78 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR T 113 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL T 76 " --> pdb=" O THR T 113 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 87 through 92 Processing sheet with id=AC8, first strand: chain 'U' and resid 7 through 10 removed outlier: 3.541A pdb=" N ARG U 9 " --> pdb=" O GLU U 28 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG U 76 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR U 81 " --> pdb=" O ASN U 52 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN U 52 " --> pdb=" O THR U 81 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 62 through 64 Processing sheet with id=AD1, first strand: chain 'V' and resid 63 through 64 removed outlier: 7.173A pdb=" N LYS V 32 " --> pdb=" O ALA V 26 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ALA V 26 " --> pdb=" O LYS V 32 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE V 34 " --> pdb=" O LEU V 24 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LYS V 8 " --> pdb=" O ILE V 71 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL V 70 " --> pdb=" O THR V 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 40 through 42 Processing sheet with id=AD3, first strand: chain 'V' and resid 81 through 83 Processing sheet with id=AD4, first strand: chain 'X' and resid 31 through 32 removed outlier: 6.623A pdb=" N LEU X 68 " --> pdb=" O LEU X 46 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 39 through 40 removed outlier: 3.516A pdb=" N LYS X 85 " --> pdb=" O LYS X 81 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 13 through 18 removed outlier: 3.637A pdb=" N THR Y 25 " --> pdb=" O ASN Y 17 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 33 through 39 Processing sheet with id=AD8, first strand: chain '0' and resid 34 through 38 Processing sheet with id=AD9, first strand: chain '2' and resid 27 through 29 Processing sheet with id=AE1, first strand: chain '2' and resid 48 through 49 removed outlier: 3.523A pdb=" N LYS 2 52 " --> pdb=" O TYR 2 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '3' and resid 15 through 22 removed outlier: 6.452A pdb=" N ARG 3 15 " --> pdb=" O CYS 3 9 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N CYS 3 9 " --> pdb=" O ARG 3 15 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR 3 17 " --> pdb=" O LEU 3 7 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '5' and resid 14 through 16 Processing sheet with id=AE4, first strand: chain '6' and resid 2 through 4 removed outlier: 6.099A pdb=" N LYS 6 2 " --> pdb=" O ARG 6 36 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL 6 23 " --> pdb=" O GLN 6 37 " (cutoff:3.500A) 701 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2324 hydrogen bonds 3718 hydrogen bond angles 0 basepair planarities 928 basepair parallelities 1531 stacking parallelities Total time for adding SS restraints: 130.12 Time building geometry restraints manager: 34.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8114 1.31 - 1.44: 40568 1.44 - 1.57: 35402 1.57 - 1.70: 5702 1.70 - 1.83: 130 Bond restraints: 89916 Sorted by residual: bond pdb=" C6 G A 903 " pdb=" N1 G A 903 " ideal model delta sigma weight residual 1.391 1.308 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" N9 G A 769 " pdb=" C4 G A 769 " ideal model delta sigma weight residual 1.375 1.306 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N9 G A1492 " pdb=" C4 G A1492 " ideal model delta sigma weight residual 1.375 1.310 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C4 C A 956 " pdb=" N4 C A 956 " ideal model delta sigma weight residual 1.335 1.271 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C ARG M 60 " pdb=" N LEU M 61 " ideal model delta sigma weight residual 1.339 1.179 0.160 5.57e-02 3.22e+02 8.28e+00 ... (remaining 89911 not shown) Histogram of bond angle deviations from ideal: 96.31 - 105.41: 14582 105.41 - 114.51: 59724 114.51 - 123.61: 47061 123.61 - 132.71: 13921 132.71 - 141.81: 266 Bond angle restraints: 135554 Sorted by residual: angle pdb=" N3 C A 956 " pdb=" C4 C A 956 " pdb=" N4 C A 956 " ideal model delta sigma weight residual 118.00 96.38 21.62 3.00e+00 1.11e-01 5.19e+01 angle pdb=" N GLY Q 52 " pdb=" CA GLY Q 52 " pdb=" C GLY Q 52 " ideal model delta sigma weight residual 110.77 121.30 -10.53 1.59e+00 3.96e-01 4.39e+01 angle pdb=" N4 C A 956 " pdb=" C4 C A 956 " pdb=" C5 C A 956 " ideal model delta sigma weight residual 120.20 138.03 -17.83 3.00e+00 1.11e-01 3.53e+01 angle pdb=" C2' G A 992 " pdb=" C1' G A 992 " pdb=" N9 G A 992 " ideal model delta sigma weight residual 114.00 106.27 7.73 1.50e+00 4.44e-01 2.65e+01 angle pdb=" O6 G A 903 " pdb=" C6 G A 903 " pdb=" N1 G A 903 " ideal model delta sigma weight residual 119.90 105.42 14.48 3.00e+00 1.11e-01 2.33e+01 ... (remaining 135549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 45033 35.82 - 71.65: 2330 71.65 - 107.47: 126 107.47 - 143.30: 10 143.30 - 179.12: 13 Dihedral angle restraints: 47512 sinusoidal: 39852 harmonic: 7660 Sorted by residual: dihedral pdb=" CA GLY D 89 " pdb=" C GLY D 89 " pdb=" N GLU D 90 " pdb=" CA GLU D 90 " ideal model delta harmonic sigma weight residual 180.00 116.80 63.20 0 5.00e+00 4.00e-02 1.60e+02 dihedral pdb=" C5' U A2811 " pdb=" C4' U A2811 " pdb=" C3' U A2811 " pdb=" O3' U A2811 " ideal model delta sinusoidal sigma weight residual 147.00 76.16 70.84 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" CA ALA S 50 " pdb=" C ALA S 50 " pdb=" N PRO S 51 " pdb=" CA PRO S 51 " ideal model delta harmonic sigma weight residual 180.00 -130.42 -49.58 0 5.00e+00 4.00e-02 9.83e+01 ... (remaining 47509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 14619 0.078 - 0.155: 2554 0.155 - 0.233: 270 0.233 - 0.311: 46 0.311 - 0.388: 11 Chirality restraints: 17500 Sorted by residual: chirality pdb=" C1' A A 654 " pdb=" O4' A A 654 " pdb=" C2' A A 654 " pdb=" N9 A A 654 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" C1' U A1093 " pdb=" O4' U A1093 " pdb=" C2' U A1093 " pdb=" N1 U A1093 " both_signs ideal model delta sigma weight residual False 2.47 2.08 0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" C1' G A2829 " pdb=" O4' G A2829 " pdb=" C2' G A2829 " pdb=" N9 G A2829 " both_signs ideal model delta sigma weight residual False 2.46 2.09 0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 17497 not shown) Planarity restraints: 6513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 992 " 0.079 2.00e-02 2.50e+03 3.41e-02 3.48e+01 pdb=" N9 G A 992 " -0.082 2.00e-02 2.50e+03 pdb=" C8 G A 992 " -0.012 2.00e-02 2.50e+03 pdb=" N7 G A 992 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 992 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G A 992 " 0.019 2.00e-02 2.50e+03 pdb=" O6 G A 992 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G A 992 " 0.012 2.00e-02 2.50e+03 pdb=" C2 G A 992 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G A 992 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G A 992 " -0.009 2.00e-02 2.50e+03 pdb=" C4 G A 992 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A2454 " -0.065 2.00e-02 2.50e+03 3.74e-02 3.15e+01 pdb=" N1 C A2454 " 0.089 2.00e-02 2.50e+03 pdb=" C2 C A2454 " -0.006 2.00e-02 2.50e+03 pdb=" O2 C A2454 " 0.005 2.00e-02 2.50e+03 pdb=" N3 C A2454 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C A2454 " -0.011 2.00e-02 2.50e+03 pdb=" N4 C A2454 " -0.014 2.00e-02 2.50e+03 pdb=" C5 C A2454 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C A2454 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 904 " 0.070 2.00e-02 2.50e+03 3.21e-02 2.84e+01 pdb=" N9 A A 904 " -0.075 2.00e-02 2.50e+03 pdb=" C8 A A 904 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A A 904 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A A 904 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A A 904 " 0.017 2.00e-02 2.50e+03 pdb=" N6 A A 904 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A A 904 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A 904 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A A 904 " -0.011 2.00e-02 2.50e+03 pdb=" C4 A A 904 " -0.015 2.00e-02 2.50e+03 ... (remaining 6510 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 590 2.57 - 3.15: 55955 3.15 - 3.74: 147596 3.74 - 4.32: 224124 4.32 - 4.90: 294648 Nonbonded interactions: 722913 Sorted by model distance: nonbonded pdb=" OG SER V 94 " pdb=" O LYS V 95 " model vdw 1.989 2.440 nonbonded pdb=" OE2 GLU 3 39 " pdb="ZN ZN 3 101 " model vdw 1.992 2.230 nonbonded pdb=" O2' C A2454 " pdb=" O5' C A2455 " model vdw 2.017 2.440 nonbonded pdb=" O6 G A1488 " pdb=" O6 G A1508 " model vdw 2.043 2.432 nonbonded pdb=" N ASP P 6 " pdb=" OD1 ASP P 6 " model vdw 2.090 2.520 ... (remaining 722908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 2855 5.49 5 S 71 5.16 5 C 40511 2.51 5 N 15251 2.21 5 O 23604 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=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: 5.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 22.650 Check model and map are aligned: 1.000 Convert atoms to be neutral: 0.560 Process input model: 297.110 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:9.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 337.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 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 : 0.011 0.160 89916 Z= 0.638 Angle : 1.148 21.620 135554 Z= 0.561 Chirality : 0.060 0.388 17500 Planarity : 0.008 0.081 6513 Dihedral : 16.562 179.124 42582 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.73 % Favored : 88.93 % Rotamer Outliers : 16.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.27 % 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: -3.84 (0.13), residues: 2647 helix: -2.43 (0.15), residues: 671 sheet: -1.70 (0.20), residues: 549 loop : -3.03 (0.13), residues: 1427 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 467 time to evaluate : 3.580 Fit side-chains revert: symmetry clash outliers start: 378 outliers final: 192 residues processed: 744 average time/residue: 1.6493 time to fit residues: 1639.2167 Evaluate side-chains 534 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 342 time to evaluate : 3.677 Switching outliers to nearest non-outliers outliers start: 192 outliers final: 165 residues processed: 29 average time/residue: 0.8717 time to fit residues: 45.0001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 456 optimal weight: 5.9990 chunk 410 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 276 optimal weight: 30.0000 chunk 219 optimal weight: 5.9990 chunk 424 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 257 optimal weight: 7.9990 chunk 315 optimal weight: 0.8980 chunk 491 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN D 68 HIS D 103 GLN D 191 ASN E 13 GLN E 75 GLN E 82 GLN E 160 ASN E 196 GLN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 ASN K 131 HIS M 38 GLN M 133 GLN N 44 ASN O 61 GLN P 12 GLN P 15 HIS P 20 ASN P 114 ASN Q 6 GLN Q 41 GLN ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 86 GLN S 88 HIS T 4 GLN T 46 ASN T 66 ASN X 49 GLN X 87 GLN Y 17 ASN Y 23 ASN Y 32 ASN Z 36 GLN 2 40 HIS 4 8 ASN 5 31 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 89916 Z= 0.228 Angle : 0.704 10.179 135554 Z= 0.369 Chirality : 0.042 0.305 17500 Planarity : 0.006 0.063 6513 Dihedral : 14.559 179.693 37197 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.24 % Favored : 91.73 % Rotamer Outliers : 11.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.16 % 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: -2.69 (0.14), residues: 2647 helix: -0.95 (0.18), residues: 698 sheet: -1.13 (0.20), residues: 595 loop : -2.61 (0.14), residues: 1354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 353 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 267 outliers final: 176 residues processed: 574 average time/residue: 1.5410 time to fit residues: 1196.6818 Evaluate side-chains 497 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 321 time to evaluate : 3.563 Switching outliers to nearest non-outliers outliers start: 176 outliers final: 155 residues processed: 22 average time/residue: 0.9772 time to fit residues: 36.8144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 273 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 408 optimal weight: 10.0000 chunk 334 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 492 optimal weight: 0.1980 chunk 531 optimal weight: 10.0000 chunk 438 optimal weight: 3.9990 chunk 488 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 394 optimal weight: 0.2980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN N 44 ASN O 61 GLN X 87 GLN Z 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 89916 Z= 0.200 Angle : 0.641 10.014 135554 Z= 0.337 Chirality : 0.039 0.286 17500 Planarity : 0.005 0.060 6513 Dihedral : 14.256 179.396 37197 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.46 % Favored : 91.50 % Rotamer Outliers : 10.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.15), residues: 2647 helix: -0.19 (0.19), residues: 705 sheet: -0.77 (0.21), residues: 591 loop : -2.37 (0.15), residues: 1351 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 331 time to evaluate : 4.320 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 236 outliers final: 172 residues processed: 523 average time/residue: 1.5961 time to fit residues: 1135.0244 Evaluate side-chains 484 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 312 time to evaluate : 3.539 Switching outliers to nearest non-outliers outliers start: 172 outliers final: 153 residues processed: 19 average time/residue: 0.8894 time to fit residues: 30.5435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 486 optimal weight: 0.0270 chunk 370 optimal weight: 0.2980 chunk 255 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 330 optimal weight: 10.0000 chunk 493 optimal weight: 6.9990 chunk 522 optimal weight: 4.9990 chunk 258 optimal weight: 10.0000 chunk 468 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 overall best weight: 2.8644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 37 ASN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN N 44 ASN O 61 GLN X 87 GLN Z 60 GLN 3 20 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 89916 Z= 0.169 Angle : 0.616 10.502 135554 Z= 0.326 Chirality : 0.038 0.283 17500 Planarity : 0.005 0.058 6513 Dihedral : 14.231 179.446 37197 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.08 % Favored : 91.88 % Rotamer Outliers : 9.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.12 % 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: -1.85 (0.15), residues: 2647 helix: 0.07 (0.19), residues: 706 sheet: -0.64 (0.21), residues: 595 loop : -2.27 (0.15), residues: 1346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 318 time to evaluate : 3.685 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 211 outliers final: 170 residues processed: 500 average time/residue: 1.5414 time to fit residues: 1052.9667 Evaluate side-chains 480 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 310 time to evaluate : 3.600 Switching outliers to nearest non-outliers outliers start: 170 outliers final: 156 residues processed: 14 average time/residue: 0.9428 time to fit residues: 24.2004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 435 optimal weight: 5.9990 chunk 296 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 389 optimal weight: 0.6980 chunk 215 optimal weight: 30.0000 chunk 446 optimal weight: 9.9990 chunk 361 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 469 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 158 ASN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN T 66 ASN X 87 GLN Z 60 GLN 3 20 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 89916 Z= 0.247 Angle : 0.685 10.059 135554 Z= 0.357 Chirality : 0.041 0.287 17500 Planarity : 0.006 0.060 6513 Dihedral : 14.301 179.569 37197 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.42 % Favored : 91.54 % Rotamer Outliers : 9.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.12 % 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: -1.73 (0.15), residues: 2647 helix: 0.14 (0.19), residues: 700 sheet: -0.44 (0.21), residues: 580 loop : -2.23 (0.15), residues: 1367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 320 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 217 outliers final: 182 residues processed: 500 average time/residue: 1.5229 time to fit residues: 1037.3359 Evaluate side-chains 495 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 313 time to evaluate : 3.559 Switching outliers to nearest non-outliers outliers start: 182 outliers final: 157 residues processed: 25 average time/residue: 1.2146 time to fit residues: 47.4258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 175 optimal weight: 10.0000 chunk 470 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 307 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 523 optimal weight: 9.9990 chunk 434 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 274 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN F 37 ASN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN M 54 GLN M 133 GLN N 44 ASN O 61 GLN R 101 ASN U 54 ASN X 87 GLN Z 48 GLN Z 60 GLN 3 20 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.095 89916 Z= 0.360 Angle : 0.817 10.595 135554 Z= 0.416 Chirality : 0.046 0.306 17500 Planarity : 0.007 0.073 6513 Dihedral : 14.604 179.603 37197 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.10 % Favored : 90.86 % Rotamer Outliers : 9.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.16 % 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: -1.86 (0.15), residues: 2647 helix: -0.12 (0.19), residues: 704 sheet: -0.42 (0.21), residues: 570 loop : -2.26 (0.15), residues: 1373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 306 time to evaluate : 3.757 Fit side-chains outliers start: 213 outliers final: 176 residues processed: 485 average time/residue: 1.5353 time to fit residues: 1024.9422 Evaluate side-chains 479 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 303 time to evaluate : 3.555 Switching outliers to nearest non-outliers outliers start: 176 outliers final: 157 residues processed: 19 average time/residue: 1.0089 time to fit residues: 33.4533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 504 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 298 optimal weight: 2.9990 chunk 382 optimal weight: 0.9990 chunk 296 optimal weight: 4.9990 chunk 440 optimal weight: 5.9990 chunk 292 optimal weight: 0.7980 chunk 521 optimal weight: 9.9990 chunk 326 optimal weight: 7.9990 chunk 317 optimal weight: 8.9990 chunk 240 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN E 46 GLN F 49 ASN M 133 GLN N 44 ASN O 61 GLN T 66 ASN X 87 GLN Z 60 GLN 2 41 HIS 3 20 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 89916 Z= 0.153 Angle : 0.597 9.923 135554 Z= 0.316 Chirality : 0.037 0.269 17500 Planarity : 0.005 0.059 6513 Dihedral : 14.107 179.355 37197 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.52 % Favored : 92.44 % Rotamer Outliers : 8.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.12 % 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: -1.49 (0.15), residues: 2647 helix: 0.39 (0.20), residues: 697 sheet: -0.27 (0.21), residues: 580 loop : -2.12 (0.15), residues: 1370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 315 time to evaluate : 4.343 Fit side-chains revert: symmetry clash outliers start: 187 outliers final: 162 residues processed: 486 average time/residue: 1.5372 time to fit residues: 1022.6382 Evaluate side-chains 470 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 308 time to evaluate : 3.625 Switching outliers to nearest non-outliers outliers start: 162 outliers final: 154 residues processed: 8 average time/residue: 1.1418 time to fit residues: 17.1571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 322 optimal weight: 8.9990 chunk 208 optimal weight: 10.0000 chunk 311 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 chunk 355 optimal weight: 20.0000 chunk 257 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 409 optimal weight: 0.9980 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN F 37 ASN N 44 ASN O 61 GLN T 66 ASN X 87 GLN Z 60 GLN 3 20 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 89916 Z= 0.345 Angle : 0.786 10.334 135554 Z= 0.401 Chirality : 0.045 0.316 17500 Planarity : 0.007 0.085 6513 Dihedral : 14.427 179.958 37197 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.92 % Favored : 91.05 % Rotamer Outliers : 8.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.12 % 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: -1.68 (0.15), residues: 2647 helix: 0.05 (0.19), residues: 706 sheet: -0.21 (0.22), residues: 555 loop : -2.20 (0.15), residues: 1386 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 308 time to evaluate : 3.596 Fit side-chains revert: symmetry clash outliers start: 197 outliers final: 173 residues processed: 484 average time/residue: 1.5562 time to fit residues: 1024.8796 Evaluate side-chains 480 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 307 time to evaluate : 3.562 Switching outliers to nearest non-outliers outliers start: 173 outliers final: 158 residues processed: 15 average time/residue: 1.2081 time to fit residues: 29.7552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 474 optimal weight: 20.0000 chunk 499 optimal weight: 6.9990 chunk 455 optimal weight: 0.9990 chunk 485 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 211 optimal weight: 10.0000 chunk 381 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 chunk 439 optimal weight: 2.9990 chunk 459 optimal weight: 4.9990 chunk 484 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN R 101 ASN T 66 ASN X 87 GLN Z 60 GLN 3 20 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 89916 Z= 0.163 Angle : 0.597 9.812 135554 Z= 0.316 Chirality : 0.037 0.270 17500 Planarity : 0.005 0.059 6513 Dihedral : 14.071 179.211 37197 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.63 % Favored : 92.33 % Rotamer Outliers : 8.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.12 % 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: -1.39 (0.16), residues: 2647 helix: 0.46 (0.20), residues: 698 sheet: -0.21 (0.21), residues: 577 loop : -2.06 (0.15), residues: 1372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 317 time to evaluate : 3.693 Fit side-chains outliers start: 180 outliers final: 163 residues processed: 485 average time/residue: 1.5438 time to fit residues: 1021.1428 Evaluate side-chains 467 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 304 time to evaluate : 3.533 Switching outliers to nearest non-outliers outliers start: 163 outliers final: 154 residues processed: 9 average time/residue: 1.2047 time to fit residues: 19.3163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 319 optimal weight: 10.0000 chunk 513 optimal weight: 9.9990 chunk 313 optimal weight: 0.0000 chunk 243 optimal weight: 10.0000 chunk 357 optimal weight: 7.9990 chunk 538 optimal weight: 0.0770 chunk 496 optimal weight: 10.0000 chunk 429 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 331 optimal weight: 9.9990 chunk 263 optimal weight: 20.0000 overall best weight: 5.6148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN F 37 ASN N 44 ASN O 61 GLN T 66 ASN Z 60 GLN 3 20 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 89916 Z= 0.273 Angle : 0.706 10.091 135554 Z= 0.366 Chirality : 0.041 0.281 17500 Planarity : 0.006 0.061 6513 Dihedral : 14.252 179.662 37197 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.58 % Favored : 91.39 % Rotamer Outliers : 7.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.12 % 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: -1.51 (0.15), residues: 2647 helix: 0.30 (0.19), residues: 699 sheet: -0.24 (0.21), residues: 580 loop : -2.11 (0.15), residues: 1368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 309 time to evaluate : 3.650 Fit side-chains outliers start: 172 outliers final: 160 residues processed: 473 average time/residue: 1.5144 time to fit residues: 984.9012 Evaluate side-chains 468 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 308 time to evaluate : 3.572 Switching outliers to nearest non-outliers outliers start: 160 outliers final: 155 residues processed: 5 average time/residue: 1.4210 time to fit residues: 13.3466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 340 optimal weight: 9.9990 chunk 457 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 395 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 429 optimal weight: 20.0000 chunk 179 optimal weight: 20.0000 chunk 441 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 133 GLN N 44 ASN O 61 GLN R 101 ASN S 83 HIS Z 60 GLN 3 20 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.090930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.078050 restraints weight = 128040.737| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 0.62 r_work: 0.2694 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.111 89916 Z= 0.456 Angle : 0.924 11.493 135554 Z= 0.463 Chirality : 0.051 0.355 17500 Planarity : 0.008 0.071 6513 Dihedral : 14.771 178.906 37197 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.44 % Favored : 90.48 % Rotamer Outliers : 7.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.19 % 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: -1.89 (0.15), residues: 2647 helix: -0.19 (0.19), residues: 698 sheet: -0.42 (0.21), residues: 577 loop : -2.27 (0.15), residues: 1372 =============================================================================== Job complete usr+sys time: 17034.96 seconds wall clock time: 300 minutes 31.89 seconds (18031.89 seconds total)