Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 14 13:26:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/10_2023/6wu9_21907.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/10_2023/6wu9_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_21907/10_2023/6wu9_21907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/10_2023/6wu9_21907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/10_2023/6wu9_21907.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/10_2023/6wu9_21907.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 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. 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 32.66, per 1000 atoms: 0.40 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: 29.99 Conformation dependent library (CDL) restraints added in 3.3 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: 27.37 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: 136.66 Time building geometry restraints manager: 32.72 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 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: 4.560 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: 0.060 Extract box with map and model: 21.090 Check model and map are aligned: 1.030 Set scattering table: 0.600 Process input model: 295.350 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 335.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 5.73 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.73 % Favored : 88.93 % Rotamer: Outliers : 16.81 % Allowed : 13.34 % Favored : 69.85 % 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 : 3.415 Fit side-chains revert: symmetry clash outliers start: 378 outliers final: 192 residues processed: 744 average time/residue: 1.7108 time to fit residues: 1684.6720 Evaluate side-chains 534 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 342 time to evaluate : 3.415 Switching outliers to nearest non-outliers outliers start: 192 outliers final: 165 residues processed: 29 average time/residue: 0.8826 time to fit residues: 45.1350 ------------------------------------------------------------------------------- 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: 0.8206 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 89916 Z= 0.238 Angle : 0.713 10.171 135554 Z= 0.372 Chirality : 0.042 0.308 17500 Planarity : 0.006 0.064 6513 Dihedral : 14.572 179.716 37197 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.35 % Favored : 91.61 % Rotamer: Outliers : 11.83 % Allowed : 20.76 % Favored : 67.41 % 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: -2.71 (0.14), residues: 2647 helix: -0.99 (0.18), residues: 699 sheet: -1.13 (0.20), residues: 585 loop : -2.60 (0.14), residues: 1363 *********************** 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 617 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 351 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 266 outliers final: 177 residues processed: 569 average time/residue: 1.6536 time to fit residues: 1268.9719 Evaluate side-chains 500 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 323 time to evaluate : 3.437 Switching outliers to nearest non-outliers outliers start: 177 outliers final: 156 residues processed: 22 average time/residue: 0.9972 time to fit residues: 38.2742 ------------------------------------------------------------------------------- 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: 8.9990 chunk 334 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 492 optimal weight: 20.0000 chunk 531 optimal weight: 9.9990 chunk 438 optimal weight: 0.0570 chunk 488 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 chunk 394 optimal weight: 10.0000 overall best weight: 7.6106 ------------------------------------------------------------------------------- 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 19 GLN G 84 GLN M 54 GLN N 44 ASN R 101 ASN S 83 HIS T 66 ASN X 87 GLN Z 60 GLN 3 20 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 89916 Z= 0.363 Angle : 0.829 10.697 135554 Z= 0.423 Chirality : 0.047 0.332 17500 Planarity : 0.007 0.068 6513 Dihedral : 14.722 179.472 37197 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.41 % Favored : 90.52 % Rotamer: Outliers : 11.43 % Allowed : 21.88 % Favored : 66.70 % 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: -2.33 (0.15), residues: 2647 helix: -0.57 (0.19), residues: 701 sheet: -0.79 (0.21), residues: 563 loop : -2.47 (0.14), residues: 1383 *********************** 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 572 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 315 time to evaluate : 3.469 Fit side-chains revert: symmetry clash outliers start: 257 outliers final: 197 residues processed: 523 average time/residue: 1.6507 time to fit residues: 1167.9930 Evaluate side-chains 504 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 307 time to evaluate : 3.533 Switching outliers to nearest non-outliers outliers start: 197 outliers final: 173 residues processed: 24 average time/residue: 1.0602 time to fit residues: 43.1351 ------------------------------------------------------------------------------- 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: 0.8980 chunk 370 optimal weight: 0.9990 chunk 255 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 330 optimal weight: 0.6980 chunk 493 optimal weight: 5.9990 chunk 522 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 chunk 468 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 G 19 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN R 101 ASN T 66 ASN X 87 GLN Z 60 GLN 2 41 HIS 5 31 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 89916 Z= 0.117 Angle : 0.552 9.687 135554 Z= 0.294 Chirality : 0.035 0.275 17500 Planarity : 0.004 0.055 6513 Dihedral : 14.057 178.617 37197 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.35 % Favored : 93.62 % Rotamer: Outliers : 9.92 % Allowed : 23.57 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % 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: -1.68 (0.15), residues: 2647 helix: 0.23 (0.20), residues: 697 sheet: -0.48 (0.21), residues: 583 loop : -2.19 (0.15), residues: 1367 *********************** 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 573 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 350 time to evaluate : 3.374 Fit side-chains outliers start: 223 outliers final: 151 residues processed: 539 average time/residue: 1.6449 time to fit residues: 1199.5710 Evaluate side-chains 469 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 318 time to evaluate : 3.422 Switching outliers to nearest non-outliers outliers start: 151 outliers final: 138 residues processed: 13 average time/residue: 0.8507 time to fit residues: 21.8343 ------------------------------------------------------------------------------- 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: 7.9990 chunk 296 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 389 optimal weight: 0.8980 chunk 215 optimal weight: 30.0000 chunk 446 optimal weight: 10.0000 chunk 361 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 469 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN G 84 GLN M 17 ASN N 44 ASN O 61 GLN S 86 GLN T 65 ASN T 66 ASN X 87 GLN Z 60 GLN 3 20 ASN 3 25 ASN 5 31 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 89916 Z= 0.266 Angle : 0.693 10.084 135554 Z= 0.359 Chirality : 0.041 0.281 17500 Planarity : 0.006 0.059 6513 Dihedral : 14.231 179.385 37197 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.54 % Favored : 91.42 % Rotamer: Outliers : 9.03 % Allowed : 24.77 % Favored : 66.21 % 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: -1.65 (0.15), residues: 2647 helix: 0.24 (0.19), residues: 697 sheet: -0.40 (0.21), residues: 579 loop : -2.20 (0.15), residues: 1371 *********************** 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 523 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 320 time to evaluate : 3.420 Fit side-chains outliers start: 203 outliers final: 168 residues processed: 493 average time/residue: 1.6353 time to fit residues: 1095.4318 Evaluate side-chains 484 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 316 time to evaluate : 3.448 Switching outliers to nearest non-outliers outliers start: 168 outliers final: 149 residues processed: 19 average time/residue: 1.0715 time to fit residues: 34.2537 ------------------------------------------------------------------------------- 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: 3.9990 chunk 103 optimal weight: 10.0000 chunk 307 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 523 optimal weight: 20.0000 chunk 434 optimal weight: 6.9990 chunk 242 optimal weight: 9.9990 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 ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 GLN N 44 ASN O 61 GLN R 101 ASN ** S 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Z 60 GLN 3 20 ASN 3 25 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1236 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= 0.359 Angle : 0.812 10.571 135554 Z= 0.414 Chirality : 0.046 0.303 17500 Planarity : 0.007 0.064 6513 Dihedral : 14.585 179.608 37197 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.22 % Favored : 90.74 % Rotamer: Outliers : 9.16 % Allowed : 24.86 % Favored : 65.98 % 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: -1.81 (0.15), residues: 2647 helix: -0.05 (0.19), residues: 700 sheet: -0.45 (0.21), residues: 578 loop : -2.22 (0.15), residues: 1369 *********************** 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 512 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 306 time to evaluate : 3.393 Fit side-chains outliers start: 206 outliers final: 163 residues processed: 485 average time/residue: 1.6162 time to fit residues: 1067.4269 Evaluate side-chains 460 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 297 time to evaluate : 3.427 Switching outliers to nearest non-outliers outliers start: 163 outliers final: 148 residues processed: 15 average time/residue: 0.8899 time to fit residues: 25.2805 ------------------------------------------------------------------------------- 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: 1.9990 chunk 382 optimal weight: 0.0770 chunk 296 optimal weight: 6.9990 chunk 440 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 chunk 521 optimal weight: 10.0000 chunk 326 optimal weight: 9.9990 chunk 317 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN R 101 ASN X 87 GLN Z 60 GLN 3 20 ASN 3 25 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 89916 Z= 0.197 Angle : 0.661 9.842 135554 Z= 0.349 Chirality : 0.040 0.279 17500 Planarity : 0.005 0.062 6513 Dihedral : 14.402 179.945 37197 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.42 % Favored : 91.54 % Rotamer: Outliers : 8.80 % Allowed : 25.08 % Favored : 66.12 % 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: -1.62 (0.15), residues: 2647 helix: 0.16 (0.19), residues: 699 sheet: -0.30 (0.21), residues: 574 loop : -2.15 (0.15), residues: 1374 *********************** 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 513 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 315 time to evaluate : 3.411 Fit side-chains outliers start: 198 outliers final: 166 residues processed: 489 average time/residue: 1.6294 time to fit residues: 1080.4311 Evaluate side-chains 475 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 309 time to evaluate : 3.358 Switching outliers to nearest non-outliers outliers start: 166 outliers final: 153 residues processed: 13 average time/residue: 1.1573 time to fit residues: 25.7185 ------------------------------------------------------------------------------- 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: 5.9990 chunk 208 optimal weight: 10.0000 chunk 311 optimal weight: 3.9990 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: 6.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- 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 ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 60 GLN 3 20 ASN 3 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 89916 Z= 0.317 Angle : 0.763 10.319 135554 Z= 0.392 Chirality : 0.044 0.302 17500 Planarity : 0.006 0.063 6513 Dihedral : 14.448 179.883 37197 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.88 % Favored : 91.08 % Rotamer: Outliers : 8.71 % Allowed : 25.57 % Favored : 65.72 % 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: -1.72 (0.15), residues: 2647 helix: 0.01 (0.19), residues: 705 sheet: -0.38 (0.21), residues: 581 loop : -2.18 (0.15), residues: 1361 *********************** 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 506 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 310 time to evaluate : 3.424 Fit side-chains outliers start: 196 outliers final: 172 residues processed: 480 average time/residue: 1.6425 time to fit residues: 1069.4305 Evaluate side-chains 477 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 305 time to evaluate : 3.387 Switching outliers to nearest non-outliers outliers start: 172 outliers final: 155 residues processed: 17 average time/residue: 1.2544 time to fit residues: 34.4077 ------------------------------------------------------------------------------- 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: 10.0000 chunk 499 optimal weight: 6.9990 chunk 455 optimal weight: 0.7980 chunk 485 optimal weight: 7.9990 chunk 292 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 381 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 439 optimal weight: 9.9990 chunk 459 optimal weight: 1.9990 chunk 484 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN G 84 GLN M 133 GLN N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 60 GLN 3 20 ASN 3 25 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 89916 Z= 0.232 Angle : 0.692 10.100 135554 Z= 0.363 Chirality : 0.041 0.277 17500 Planarity : 0.006 0.093 6513 Dihedral : 14.414 179.870 37197 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.54 % Favored : 91.42 % Rotamer: Outliers : 8.00 % Allowed : 25.83 % Favored : 66.16 % 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: -1.63 (0.15), residues: 2647 helix: 0.15 (0.19), residues: 699 sheet: -0.30 (0.21), residues: 571 loop : -2.16 (0.15), residues: 1377 *********************** 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 490 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 310 time to evaluate : 3.471 Fit side-chains outliers start: 180 outliers final: 165 residues processed: 474 average time/residue: 1.6866 time to fit residues: 1080.8988 Evaluate side-chains 469 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 304 time to evaluate : 3.470 Switching outliers to nearest non-outliers outliers start: 165 outliers final: 155 residues processed: 10 average time/residue: 1.2613 time to fit residues: 21.5895 ------------------------------------------------------------------------------- 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: 2.9990 chunk 513 optimal weight: 0.8980 chunk 313 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 chunk 357 optimal weight: 0.9990 chunk 538 optimal weight: 4.9990 chunk 496 optimal weight: 2.9990 chunk 429 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 331 optimal weight: 9.9990 chunk 263 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 60 GLN 3 20 ASN 3 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 89916 Z= 0.153 Angle : 0.619 10.102 135554 Z= 0.329 Chirality : 0.038 0.321 17500 Planarity : 0.005 0.063 6513 Dihedral : 14.306 179.804 37197 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.05 % Favored : 91.92 % Rotamer: Outliers : 7.65 % Allowed : 26.50 % Favored : 65.85 % 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: -1.46 (0.15), residues: 2647 helix: 0.37 (0.19), residues: 698 sheet: -0.24 (0.21), residues: 575 loop : -2.08 (0.15), residues: 1374 ********************** 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 483 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 311 time to evaluate : 3.698 Fit side-chains outliers start: 172 outliers final: 157 residues processed: 472 average time/residue: 1.6493 time to fit residues: 1057.6243 Evaluate side-chains 462 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 305 time to evaluate : 3.365 Switching outliers to nearest non-outliers outliers start: 157 outliers final: 152 residues processed: 5 average time/residue: 1.4432 time to fit residues: 13.4390 ------------------------------------------------------------------------------- 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: 20.0000 chunk 457 optimal weight: 0.8980 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: 7.9990 chunk 179 optimal weight: 20.0000 chunk 441 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 overall best weight: 5.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN E 158 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 GLN N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 60 GLN 3 20 ASN 3 25 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.092763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.079905 restraints weight = 127237.313| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 0.58 r_work: 0.2725 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 89916 Z= 0.291 Angle : 0.730 10.191 135554 Z= 0.377 Chirality : 0.043 0.294 17500 Planarity : 0.006 0.063 6513 Dihedral : 14.358 179.825 37197 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.76 % Favored : 91.20 % Rotamer: Outliers : 8.00 % Allowed : 26.14 % Favored : 65.85 % 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: -1.57 (0.15), residues: 2647 helix: 0.20 (0.19), residues: 699 sheet: -0.24 (0.21), residues: 572 loop : -2.13 (0.15), residues: 1376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17996.06 seconds wall clock time: 317 minutes 40.81 seconds (19060.81 seconds total)