Starting phenix.real_space_refine (version: dev) on Mon May 16 23:20:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/05_2022/6xz7_10655_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/05_2022/6xz7_10655.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/05_2022/6xz7_10655_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/05_2022/6xz7_10655_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/05_2022/6xz7_10655_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/05_2022/6xz7_10655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/05_2022/6xz7_10655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/05_2022/6xz7_10655_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/05_2022/6xz7_10655_updated.pdb" } resolution = 2.1 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= 0.037 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 "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 94915 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 62252 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2897, 62209 Classifications: {'RNA': 2897} Modifications used: {'rna3p': 17, 'rna2p': 7, 'rna3p_pur': 1387, 'rna3p_pyr': 1063, 'rna2p_pur': 277, 'rna2p_pyr': 146} Link IDs: {'rna3p': 2467, 'rna2p': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Conformer: "B" Number of residues, atoms: 2897, 62209 Classifications: {'RNA': 2897} Modifications used: {'rna3p': 17, 'rna2p': 7, 'rna3p_pur': 1387, 'rna3p_pyr': 1063, 'rna2p_pur': 277, 'rna2p_pyr': 146} Link IDs: {'rna3p': 2467, 'rna2p': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 bond proxies already assigned to first conformer: 69623 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna3p_pyr': 50, 'rna2p_pur': 7, 'rna3p_pur': 57, 'rna2p_pyr': 6} Link IDs: {'rna3p': 106, 'rna2p': 13} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1023 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "I" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 979 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1075 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 993 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "O" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 580 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "b" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "d" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "e" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "f" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna3p_pyr': 29, 'rna2p_pur': 6, 'rna3p_pur': 33, 'rna2p_pyr': 4, 'rna3p': 4} Link IDs: {'rna3p': 66, 'rna2p': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "g" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1667 Classifications: {'RNA': 75, 'peptide': 1} Modifications used: {'5*END': 1, 'rna3p': 12, 'rna2p_pyr': 4, 'rna3p_pur': 30, 'rna2p': 2, 'rna3p_pyr': 23, 'rna2p_pur': 4} Link IDs: {None: 1, 'rna3p': 64, 'rna2p': 10} Not linked: pdbres=" C g 75 " pdbres="31M g 76 " Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 232 Unusual residues: {' MG': 174, 'DI0': 1} Classifications: {'undetermined': 175} Link IDs: {None: 174} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 498 Classifications: {'water': 498} Link IDs: {None: 497} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" P A C A2888 " occ=0.53 ... (38 atoms not shown) pdb=" C6 B C A2888 " occ=0.47 residue: pdb=" N AMEQ D 150 " occ=0.49 ... (8 atoms not shown) pdb=" NE2AMEQ D 150 " occ=0.49 residue: pdb=" N AARG W 41 " occ=0.51 ... (9 atoms not shown) pdb=" NH2AARG W 41 " occ=0.51 residue: pdb=" N AALA Z 2 " occ=0.50 ... (3 atoms not shown) pdb=" CB AALA Z 2 " occ=0.50 residue: pdb=" N ALYS Z 3 " occ=0.50 ... (7 atoms not shown) pdb=" NZ ALYS Z 3 " occ=0.50 Time building chain proxies: 65.11, per 1000 atoms: 0.69 Number of scatterers: 94915 At special positions: 0 Unit cell: (251.12, 227.9, 208.12, 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) S 85 16.00 P 3170 15.00 Mg 178 11.99 O 27197 8.00 N 17508 7.00 C 46777 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 41.81 Conformation dependent library (CDL) restraints added in 4.6 seconds 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 49 sheets defined 27.7% alpha, 19.8% beta 1041 base pairs and 1710 stacking pairs defined. Time for finding SS restraints: 49.00 Creating SS restraints... Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.920A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.819A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.525A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 101 Processing helix chain 'D' and resid 121 through 125 Processing helix chain 'E' and resid 16 through 19 No H-bonds generated for 'chain 'E' and resid 16 through 19' Processing helix chain 'E' and resid 25 through 39 Processing helix chain 'E' and resid 98 through 114 Processing helix chain 'E' and resid 131 through 140 Processing helix chain 'E' and resid 155 through 160 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 177 through 182 removed outlier: 3.575A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.550A pdb=" N ASP F 10 " --> pdb=" O ASP F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 19 removed outlier: 3.576A pdb=" N THR F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 42 through 44 No H-bonds generated for 'chain 'F' and resid 42 through 44' Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.874A pdb=" N ASN F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 104 removed outlier: 3.708A pdb=" N ARG F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE F 104 " --> pdb=" O PHE F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 172 Processing helix chain 'G' and resid 59 through 80 removed outlier: 4.573A pdb=" N TRP G 62 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY G 66 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG G 69 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU G 72 " --> pdb=" O ARG G 69 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN G 73 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL G 76 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL G 79 " --> pdb=" O VAL G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 Processing helix chain 'H' and resid 5 through 21 removed outlier: 3.571A pdb=" N GLY H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 47 Processing helix chain 'H' and resid 57 through 65 removed outlier: 3.744A pdb=" N ALA H 63 " --> pdb=" O LEU H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 75 removed outlier: 3.888A pdb=" N ASP H 74 " --> pdb=" O CYS H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 103 removed outlier: 3.665A pdb=" N LYS H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU H 98 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 removed outlier: 3.740A pdb=" N ASP H 124 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA H 127 " --> pdb=" O ASP H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 134 No H-bonds generated for 'chain 'H' and resid 132 through 134' Processing helix chain 'I' and resid 25 through 31 removed outlier: 4.635A pdb=" N GLN I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 48 removed outlier: 5.220A pdb=" N SER I 48 " --> pdb=" O ALA I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 83 Processing helix chain 'I' and resid 103 through 116 Processing helix chain 'I' and resid 122 through 135 Processing helix chain 'J' and resid 25 through 37 removed outlier: 4.034A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 89 through 95 Processing helix chain 'J' and resid 97 through 108 removed outlier: 4.234A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.917A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 135 No H-bonds generated for 'chain 'J' and resid 133 through 135' Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 118 Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 79 through 81 No H-bonds generated for 'chain 'L' and resid 79 through 81' Processing helix chain 'L' and resid 92 through 97 Processing helix chain 'L' and resid 129 through 138 Processing helix chain 'M' and resid 43 through 56 Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.603A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 56 removed outlier: 4.270A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 73 through 81 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 122 through 124 No H-bonds generated for 'chain 'N' and resid 122 through 124' Processing helix chain 'O' and resid 3 through 21 removed outlier: 3.537A pdb=" N ARG O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 61 removed outlier: 5.846A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 83 Processing helix chain 'O' and resid 102 through 112 Processing helix chain 'P' and resid 3 through 10 Processing helix chain 'P' and resid 54 through 56 No H-bonds generated for 'chain 'P' and resid 54 through 56' Processing helix chain 'P' and resid 98 through 102 Processing helix chain 'P' and resid 105 through 108 Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.568A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 29 Processing helix chain 'Q' and resid 32 through 72 removed outlier: 3.651A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 85 Processing helix chain 'Q' and resid 92 through 101 Processing helix chain 'Q' and resid 103 through 117 Processing helix chain 'S' and resid 14 through 24 removed outlier: 3.762A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 37 removed outlier: 3.574A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 60 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 4 through 10 removed outlier: 3.980A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 26 Processing helix chain 'T' and resid 40 through 50 Processing helix chain 'U' and resid 51 through 53 No H-bonds generated for 'chain 'U' and resid 51 through 53' Processing helix chain 'U' and resid 67 through 69 No H-bonds generated for 'chain 'U' and resid 67 through 69' Processing helix chain 'V' and resid 14 through 23 Processing helix chain 'V' and resid 44 through 52 removed outlier: 3.533A pdb=" N MET V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 57 Processing helix chain 'X' and resid 53 through 62 Processing helix chain 'X' and resid 64 through 74 Processing helix chain 'Y' and resid 6 through 8 No H-bonds generated for 'chain 'Y' and resid 6 through 8' Processing helix chain 'Y' and resid 11 through 34 Processing helix chain 'Y' and resid 40 through 62 removed outlier: 3.726A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP Y 49 " --> pdb=" O VAL Y 46 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL Y 50 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS Y 54 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU Y 57 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS Y 60 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA Y 61 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 27 Processing helix chain 'Z' and resid 42 through 50 Processing helix chain 'a' and resid 10 through 19 removed outlier: 4.811A pdb=" N HIS a 19 " --> pdb=" O MET a 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 16 Processing helix chain 'c' and resid 18 through 23 Processing helix chain 'c' and resid 25 through 37 Processing helix chain 'd' and resid 8 through 11 No H-bonds generated for 'chain 'd' and resid 8 through 11' Processing helix chain 'd' and resid 38 through 44 Processing helix chain 'd' and resid 52 through 61 removed outlier: 4.784A pdb=" N GLY d 56 " --> pdb=" O GLY d 53 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE d 59 " --> pdb=" O GLY d 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 33 No H-bonds generated for 'chain 'e' and resid 31 through 33' Processing sheet with id= A, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'C' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.641A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL C 78 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 129 through 131 Processing sheet with id= E, first strand: chain 'C' and resid 181 through 185 removed outlier: 3.528A pdb=" N ALA C 166 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG C 175 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 169 through 172 removed outlier: 4.772A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D 15 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL D 20 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 79 through 83 removed outlier: 6.371A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 115 through 119 removed outlier: 5.725A pdb=" N MET D 165 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE D 118 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLY D 163 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 2 through 4 Processing sheet with id= J, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.131A pdb=" N VAL E 186 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL E 121 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N MET E 188 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 128 through 132 removed outlier: 3.590A pdb=" N THR F 155 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR F 35 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR F 68 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS F 87 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU F 66 " --> pdb=" O CYS F 87 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 16 through 20 Processing sheet with id= M, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= N, first strand: chain 'G' and resid 161 through 164 removed outlier: 3.544A pdb=" N ARG G 163 " --> pdb=" O GLN G 88 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.615A pdb=" N ARG G 95 " --> pdb=" O SER G 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL G 113 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.907A pdb=" N SER H 24 " --> pdb=" O VAL H 85 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 111 through 113 Processing sheet with id= R, first strand: chain 'I' and resid 9 through 14 Processing sheet with id= S, first strand: chain 'J' and resid 15 through 19 removed outlier: 6.708A pdb=" N TYR J 53 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL J 18 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE J 55 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 73 through 77 Processing sheet with id= U, first strand: chain 'K' and resid 7 through 9 removed outlier: 6.474A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 74 through 78 removed outlier: 6.636A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE L 77 " --> pdb=" O PHE L 107 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS L 109 " --> pdb=" O ILE L 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'L' and resid 121 through 123 removed outlier: 6.477A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'M' and resid 128 through 132 removed outlier: 3.698A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 39 through 42 removed outlier: 6.945A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TRP M 92 " --> pdb=" O LYS M 71 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS M 71 " --> pdb=" O TRP M 92 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= AA, first strand: chain 'O' and resid 91 through 93 removed outlier: 3.788A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'P' and resid 83 through 88 removed outlier: 6.800A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N GLU P 44 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE P 64 " --> pdb=" O GLU P 44 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR P 60 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE P 50 " --> pdb=" O ALA P 58 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA P 58 " --> pdb=" O ILE P 50 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'R' and resid 10 through 15 removed outlier: 7.299A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'R' and resid 19 through 23 Processing sheet with id= AE, first strand: chain 'R' and resid 32 through 35 removed outlier: 6.425A pdb=" N GLU R 62 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE R 98 " --> pdb=" O GLU R 62 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.149A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'S' and resid 3 through 7 removed outlier: 6.808A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'S' and resid 82 through 87 Processing sheet with id= AI, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.615A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'T' and resid 67 through 70 Processing sheet with id= AK, first strand: chain 'U' and resid 22 through 24 removed outlier: 6.076A pdb=" N GLU U 10 " --> pdb=" O PHE U 73 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE U 72 " --> pdb=" O ASP U 81 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'U' and resid 41 through 46 Processing sheet with id= AM, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= AN, first strand: chain 'U' and resid 25 through 28 removed outlier: 6.802A pdb=" N ILE U 35 " --> pdb=" O LYS U 26 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'V' and resid 62 through 65 removed outlier: 7.988A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE V 89 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N TYR V 31 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE V 91 " --> pdb=" O TYR V 31 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'W' and resid 51 through 53 Processing sheet with id= AQ, first strand: chain 'W' and resid 66 through 72 Processing sheet with id= AR, first strand: chain 'X' and resid 13 through 18 Processing sheet with id= AS, first strand: chain 'X' and resid 33 through 40 Processing sheet with id= AT, first strand: chain 'Z' and resid 35 through 39 Processing sheet with id= AU, first strand: chain 'b' and resid 20 through 25 Processing sheet with id= AV, first strand: chain 'e' and resid 2 through 4 Processing sheet with id= AW, first strand: chain 'e' and resid 14 through 19 873 hydrogen bonds defined for protein. 2355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2614 hydrogen bonds 4046 hydrogen bond angles 0 basepair planarities 1041 basepair parallelities 1712 stacking parallelities Total time for adding SS restraints: 305.63 Time building geometry restraints manager: 45.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 7234 1.27 - 1.40: 32553 1.40 - 1.54: 56259 1.54 - 1.68: 6524 1.68 - 1.82: 153 Bond restraints: 102723 Sorted by residual: bond pdb=" O3' 3TD A1915 " pdb=" P A A1916 " ideal model delta sigma weight residual 1.607 1.315 0.292 1.50e-02 4.44e+03 3.80e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.805 1.422 0.383 2.00e-02 2.50e+03 3.66e+02 bond pdb=" C4 5MU A 747 " pdb=" C5 5MU A 747 " ideal model delta sigma weight residual 1.805 1.424 0.381 2.00e-02 2.50e+03 3.62e+02 bond pdb=" C4 5MU f 54 " pdb=" C5 5MU f 54 " ideal model delta sigma weight residual 1.805 1.427 0.378 2.00e-02 2.50e+03 3.58e+02 bond pdb=" C4 5MU g 54 " pdb=" C5 5MU g 54 " ideal model delta sigma weight residual 1.805 1.463 0.342 2.00e-02 2.50e+03 2.93e+02 ... (remaining 102718 not shown) Histogram of bond angle deviations from ideal: 86.98 - 97.95: 38 97.95 - 108.92: 40384 108.92 - 119.89: 71889 119.89 - 130.86: 41120 130.86 - 141.83: 1003 Bond angle restraints: 154434 Sorted by residual: angle pdb=" C3' 3TD A1915 " pdb=" O3' 3TD A1915 " pdb=" P A A1916 " ideal model delta sigma weight residual 120.20 89.07 31.13 1.50e+00 4.44e-01 4.31e+02 angle pdb=" O2' C f 51 " pdb=" C2' C f 51 " pdb=" C1' C f 51 " ideal model delta sigma weight residual 108.40 86.98 21.42 1.50e+00 4.44e-01 2.04e+02 angle pdb=" O2' C f 40 " pdb=" C2' C f 40 " pdb=" C1' C f 40 " ideal model delta sigma weight residual 108.40 87.97 20.43 1.50e+00 4.44e-01 1.86e+02 angle pdb=" C4' U g 47 " pdb=" C3' U g 47 " pdb=" O3' U g 47 " ideal model delta sigma weight residual 109.40 129.72 -20.32 1.50e+00 4.44e-01 1.84e+02 angle pdb=" C4' C g 13 " pdb=" C3' C g 13 " pdb=" O3' C g 13 " ideal model delta sigma weight residual 113.00 132.66 -19.66 1.50e+00 4.44e-01 1.72e+02 ... (remaining 154429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 52257 35.85 - 71.71: 1869 71.71 - 107.56: 169 107.56 - 143.41: 17 143.41 - 179.26: 9 Dihedral angle restraints: 54321 sinusoidal: 44820 harmonic: 9501 Sorted by residual: dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 23.09 176.91 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A1779 " pdb=" C1' U A1779 " pdb=" N1 U A1779 " pdb=" C2 U A1779 " ideal model delta sinusoidal sigma weight residual 200.00 57.47 142.53 1 1.50e+01 4.44e-03 7.65e+01 dihedral pdb=" O4' U A2321 " pdb=" C1' U A2321 " pdb=" N1 U A2321 " pdb=" C2 U A2321 " ideal model delta sinusoidal sigma weight residual 200.00 60.67 139.33 1 1.50e+01 4.44e-03 7.50e+01 ... (remaining 54318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 19569 0.195 - 0.390: 124 0.390 - 0.585: 23 0.585 - 0.780: 6 0.780 - 0.975: 2 Chirality restraints: 19724 Sorted by residual: chirality pdb=" C3' C g 13 " pdb=" C4' C g 13 " pdb=" O3' C g 13 " pdb=" C2' C g 13 " both_signs ideal model delta sigma weight residual False -2.48 -1.50 -0.97 2.00e-01 2.50e+01 2.37e+01 chirality pdb=" C2' G g 18 " pdb=" C3' G g 18 " pdb=" O2' G g 18 " pdb=" C1' G g 18 " both_signs ideal model delta sigma weight residual False -2.52 -1.72 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C3' U g 47 " pdb=" C4' U g 47 " pdb=" O3' U g 47 " pdb=" C2' U g 47 " both_signs ideal model delta sigma weight residual False -2.74 -1.97 -0.77 2.00e-01 2.50e+01 1.50e+01 ... (remaining 19721 not shown) Planarity restraints: 7764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 1MA g 58 " 0.876 2.00e-02 2.50e+03 6.96e-01 1.09e+04 pdb=" C4' 1MA g 58 " -0.306 2.00e-02 2.50e+03 pdb=" O4' 1MA g 58 " -0.433 2.00e-02 2.50e+03 pdb=" C3' 1MA g 58 " -0.098 2.00e-02 2.50e+03 pdb=" O3' 1MA g 58 " -1.346 2.00e-02 2.50e+03 pdb=" C2' 1MA g 58 " 0.737 2.00e-02 2.50e+03 pdb=" O2' 1MA g 58 " 0.932 2.00e-02 2.50e+03 pdb=" C1' 1MA g 58 " -0.241 2.00e-02 2.50e+03 pdb=" N9 1MA g 58 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG g 10 " -0.001 2.00e-02 2.50e+03 6.54e-01 9.62e+03 pdb=" C4' 2MG g 10 " 0.476 2.00e-02 2.50e+03 pdb=" O4' 2MG g 10 " 0.766 2.00e-02 2.50e+03 pdb=" C3' 2MG g 10 " -0.561 2.00e-02 2.50e+03 pdb=" O3' 2MG g 10 " -0.686 2.00e-02 2.50e+03 pdb=" C2' 2MG g 10 " -0.188 2.00e-02 2.50e+03 pdb=" O2' 2MG g 10 " 1.063 2.00e-02 2.50e+03 pdb=" C1' 2MG g 10 " 0.160 2.00e-02 2.50e+03 pdb=" N9 2MG g 10 " -1.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' YYG g 37 " 0.072 2.00e-02 2.50e+03 6.35e-01 9.06e+03 pdb=" C4' YYG g 37 " 0.367 2.00e-02 2.50e+03 pdb=" O4' YYG g 37 " 0.596 2.00e-02 2.50e+03 pdb=" C3' YYG g 37 " -0.703 2.00e-02 2.50e+03 pdb=" O3' YYG g 37 " -0.642 2.00e-02 2.50e+03 pdb=" C2' YYG g 37 " -0.116 2.00e-02 2.50e+03 pdb=" O2' YYG g 37 " 1.107 2.00e-02 2.50e+03 pdb=" C1' YYG g 37 " 0.272 2.00e-02 2.50e+03 pdb=" N9 YYG g 37 " -0.954 2.00e-02 2.50e+03 ... (remaining 7761 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 397 2.23 - 2.90: 34443 2.90 - 3.57: 150445 3.57 - 4.23: 315400 4.23 - 4.90: 405152 Nonbonded interactions: 905837 Sorted by model distance: nonbonded pdb=" N2 G A 883 " pdb=" O2 U A 894 " model vdw 1.564 2.496 nonbonded pdb=" OP1 A A2268 " pdb="MG MG A3044 " model vdw 1.586 2.170 nonbonded pdb=" OP1 A A 751 " pdb="MG MG A3012 " model vdw 1.589 2.170 nonbonded pdb=" OP2 A A1189 " pdb="MG MG A3088 " model vdw 1.606 2.170 nonbonded pdb=" OP2 G A1828 " pdb="MG MG A3072 " model vdw 1.620 2.170 ... (remaining 905832 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 P 3170 5.49 5 Mg 178 5.21 5 S 85 5.16 5 C 46777 2.51 5 N 17508 2.21 5 O 27197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 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: 11.900 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: 0.120 Extract box with map and model: 31.830 Check model and map are aligned: 1.130 Convert atoms to be neutral: 0.640 Process input model: 523.050 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:15.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 586.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 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 : 0.010 0.383 102723 Z= 0.581 Angle : 0.811 38.533 154434 Z= 0.475 Chirality : 0.049 0.975 19724 Planarity : 0.031 0.696 7764 Dihedral : 14.527 179.265 48203 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.83 % Favored : 96.78 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.13), residues: 3287 helix: -2.05 (0.13), residues: 904 sheet: -1.33 (0.18), residues: 695 loop : -1.04 (0.14), residues: 1688 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 642 time to evaluate : 4.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 32 residues processed: 708 average time/residue: 2.0003 time to fit residues: 1859.5646 Evaluate side-chains 577 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 545 time to evaluate : 4.109 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 6 average time/residue: 1.1340 time to fit residues: 14.6343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 537 optimal weight: 2.9990 chunk 482 optimal weight: 0.6980 chunk 267 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 325 optimal weight: 1.9990 chunk 257 optimal weight: 0.6980 chunk 499 optimal weight: 6.9990 chunk 193 optimal weight: 0.6980 chunk 303 optimal weight: 1.9990 chunk 371 optimal weight: 7.9990 chunk 578 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN D 42 ASN G 104 ASN G 111 HIS N 18 GLN N 23 ASN P 7 GLN P 41 GLN P 75 GLN T 70 HIS U 66 GLN Y 58 ASN Z 49 ASN c 26 ASN d 28 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 102723 Z= 0.172 Angle : 0.711 14.690 154434 Z= 0.396 Chirality : 0.036 0.364 19724 Planarity : 0.008 0.136 7764 Dihedral : 14.186 179.793 41685 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.34 % Favored : 97.54 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3287 helix: -0.23 (0.16), residues: 934 sheet: -0.67 (0.18), residues: 694 loop : -0.48 (0.14), residues: 1659 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 550 time to evaluate : 4.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 49 residues processed: 612 average time/residue: 1.9119 time to fit residues: 1563.5967 Evaluate side-chains 585 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 536 time to evaluate : 4.101 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 37 residues processed: 13 average time/residue: 0.8555 time to fit residues: 23.3085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 321 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 chunk 481 optimal weight: 2.9990 chunk 393 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 579 optimal weight: 2.9990 chunk 626 optimal weight: 50.0000 chunk 516 optimal weight: 5.9990 chunk 574 optimal weight: 0.4980 chunk 197 optimal weight: 5.9990 chunk 464 optimal weight: 7.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN N 18 GLN N 23 ASN Q 59 GLN U 74 ASN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 102723 Z= 0.275 Angle : 0.773 16.643 154434 Z= 0.423 Chirality : 0.039 0.407 19724 Planarity : 0.009 0.150 7764 Dihedral : 14.038 179.644 41685 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.40 % Favored : 97.47 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3287 helix: 0.32 (0.17), residues: 936 sheet: -0.36 (0.19), residues: 673 loop : -0.32 (0.14), residues: 1678 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 541 time to evaluate : 4.315 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 62 residues processed: 603 average time/residue: 1.9455 time to fit residues: 1569.0150 Evaluate side-chains 589 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 527 time to evaluate : 4.134 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 40 residues processed: 22 average time/residue: 1.2290 time to fit residues: 45.3621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 572 optimal weight: 10.0000 chunk 435 optimal weight: 7.9990 chunk 300 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 276 optimal weight: 6.9990 chunk 389 optimal weight: 4.9990 chunk 581 optimal weight: 4.9990 chunk 615 optimal weight: 0.0170 chunk 303 optimal weight: 1.9990 chunk 551 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN C 243 HIS F 37 ASN N 18 GLN N 23 ASN P 75 GLN Q 59 GLN Q 72 ASN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 102723 Z= 0.319 Angle : 0.804 17.117 154434 Z= 0.436 Chirality : 0.041 0.407 19724 Planarity : 0.009 0.153 7764 Dihedral : 13.954 179.915 41685 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.22 % Favored : 97.66 % Rotamer Outliers : 3.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3287 helix: 0.48 (0.17), residues: 933 sheet: -0.31 (0.18), residues: 705 loop : -0.17 (0.15), residues: 1649 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 528 time to evaluate : 4.324 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 63 residues processed: 595 average time/residue: 1.9491 time to fit residues: 1548.4060 Evaluate side-chains 581 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 518 time to evaluate : 4.209 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 42 residues processed: 21 average time/residue: 1.3773 time to fit residues: 47.3752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 512 optimal weight: 6.9990 chunk 349 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 458 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 525 optimal weight: 10.0000 chunk 425 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 314 optimal weight: 0.6980 chunk 552 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN C 142 HIS K 29 HIS N 18 GLN P 75 GLN Q 59 GLN R 86 GLN U 66 GLN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.087 102723 Z= 0.430 Angle : 0.896 19.824 154434 Z= 0.473 Chirality : 0.045 0.393 19724 Planarity : 0.010 0.162 7764 Dihedral : 13.963 178.669 41685 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.46 % Favored : 97.41 % Rotamer Outliers : 3.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3287 helix: 0.45 (0.17), residues: 935 sheet: -0.28 (0.18), residues: 697 loop : -0.16 (0.15), residues: 1655 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 533 time to evaluate : 5.322 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 68 residues processed: 604 average time/residue: 1.9227 time to fit residues: 1551.3485 Evaluate side-chains 601 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 533 time to evaluate : 4.139 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 48 residues processed: 20 average time/residue: 1.0785 time to fit residues: 38.2517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 207 optimal weight: 4.9990 chunk 554 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 361 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 616 optimal weight: 1.9990 chunk 511 optimal weight: 1.9990 chunk 285 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 323 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN K 29 HIS N 18 GLN P 75 GLN Q 59 GLN Q 72 ASN R 86 GLN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 102723 Z= 0.317 Angle : 0.799 17.068 154434 Z= 0.433 Chirality : 0.040 0.393 19724 Planarity : 0.009 0.152 7764 Dihedral : 13.912 179.947 41685 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.25 % Favored : 97.63 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3287 helix: 0.61 (0.17), residues: 934 sheet: -0.22 (0.18), residues: 705 loop : -0.10 (0.15), residues: 1648 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 525 time to evaluate : 4.214 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 70 residues processed: 592 average time/residue: 1.9921 time to fit residues: 1565.9723 Evaluate side-chains 592 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 522 time to evaluate : 4.142 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 52 residues processed: 18 average time/residue: 1.1572 time to fit residues: 36.4766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 594 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 351 optimal weight: 2.9990 chunk 450 optimal weight: 2.9990 chunk 348 optimal weight: 0.0020 chunk 518 optimal weight: 0.9990 chunk 344 optimal weight: 2.9990 chunk 613 optimal weight: 0.5980 chunk 384 optimal weight: 7.9990 chunk 374 optimal weight: 9.9990 chunk 283 optimal weight: 6.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN K 29 HIS K 90 ASN N 18 GLN P 75 GLN Q 59 GLN Q 72 ASN R 86 GLN U 66 GLN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 102723 Z= 0.156 Angle : 0.691 14.482 154434 Z= 0.392 Chirality : 0.035 0.389 19724 Planarity : 0.008 0.137 7764 Dihedral : 13.920 178.041 41685 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.34 % Favored : 97.54 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3287 helix: 0.81 (0.17), residues: 934 sheet: -0.22 (0.18), residues: 706 loop : -0.06 (0.15), residues: 1647 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 537 time to evaluate : 4.362 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 60 residues processed: 596 average time/residue: 1.9665 time to fit residues: 1556.8065 Evaluate side-chains 587 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 527 time to evaluate : 4.275 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 53 residues processed: 7 average time/residue: 1.1919 time to fit residues: 17.1192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 379 optimal weight: 20.0000 chunk 245 optimal weight: 6.9990 chunk 366 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 390 optimal weight: 6.9990 chunk 418 optimal weight: 40.0000 chunk 303 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 482 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN K 29 HIS N 18 GLN P 75 GLN Q 71 GLN Q 72 ASN R 86 GLN U 54 GLN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.090 102723 Z= 0.468 Angle : 0.924 20.129 154434 Z= 0.483 Chirality : 0.046 0.376 19724 Planarity : 0.010 0.165 7764 Dihedral : 13.932 178.342 41685 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.53 % Favored : 97.35 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3287 helix: 0.59 (0.17), residues: 936 sheet: -0.22 (0.18), residues: 697 loop : -0.10 (0.15), residues: 1654 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 531 time to evaluate : 4.329 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 68 residues processed: 592 average time/residue: 2.0744 time to fit residues: 1643.9247 Evaluate side-chains 595 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 527 time to evaluate : 4.329 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 48 residues processed: 20 average time/residue: 1.1522 time to fit residues: 41.0590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 558 optimal weight: 1.9990 chunk 588 optimal weight: 4.9990 chunk 536 optimal weight: 1.9990 chunk 572 optimal weight: 5.9990 chunk 344 optimal weight: 0.9990 chunk 249 optimal weight: 0.9980 chunk 449 optimal weight: 0.6980 chunk 175 optimal weight: 5.9990 chunk 517 optimal weight: 1.9990 chunk 541 optimal weight: 3.9990 chunk 570 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN K 29 HIS N 18 GLN P 75 GLN Q 72 ASN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 102723 Z= 0.169 Angle : 0.685 14.779 154434 Z= 0.389 Chirality : 0.035 0.374 19724 Planarity : 0.008 0.136 7764 Dihedral : 13.830 177.783 41685 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.19 % Favored : 97.69 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3287 helix: 0.85 (0.17), residues: 940 sheet: -0.12 (0.19), residues: 698 loop : 0.00 (0.15), residues: 1649 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 533 time to evaluate : 4.180 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 59 residues processed: 590 average time/residue: 1.9606 time to fit residues: 1538.1123 Evaluate side-chains 586 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 527 time to evaluate : 4.163 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 52 residues processed: 8 average time/residue: 1.0175 time to fit residues: 17.4591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 375 optimal weight: 0.9980 chunk 605 optimal weight: 4.9990 chunk 369 optimal weight: 5.9990 chunk 287 optimal weight: 7.9990 chunk 420 optimal weight: 40.0000 chunk 634 optimal weight: 40.0000 chunk 584 optimal weight: 10.0000 chunk 505 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 390 optimal weight: 5.9990 chunk 309 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN K 29 HIS N 18 GLN P 75 GLN Q 71 GLN Q 72 ASN U 66 GLN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 102723 Z= 0.318 Angle : 0.797 17.172 154434 Z= 0.433 Chirality : 0.040 0.394 19724 Planarity : 0.009 0.154 7764 Dihedral : 13.830 179.963 41685 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.28 % Favored : 97.60 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3287 helix: 0.78 (0.17), residues: 937 sheet: -0.14 (0.19), residues: 698 loop : -0.00 (0.15), residues: 1652 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 521 time to evaluate : 4.157 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 55 residues processed: 575 average time/residue: 2.0922 time to fit residues: 1594.7403 Evaluate side-chains 570 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 515 time to evaluate : 4.091 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 50 residues processed: 5 average time/residue: 1.1930 time to fit residues: 13.4841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 401 optimal weight: 9.9990 chunk 538 optimal weight: 0.1980 chunk 154 optimal weight: 7.9990 chunk 465 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 506 optimal weight: 0.8980 chunk 211 optimal weight: 90.0000 chunk 519 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN E 90 GLN F 5 HIS K 29 HIS N 18 GLN P 75 GLN Q 71 GLN Q 72 ASN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.177045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135790 restraints weight = 124590.965| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 0.49 r_work: 0.3394 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work: 0.3279 rms_B_bonded: 2.02 restraints_weight: 0.1250 r_work: 0.3165 rms_B_bonded: 3.21 restraints_weight: 0.0625 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 102723 Z= 0.198 Angle : 0.710 15.367 154434 Z= 0.398 Chirality : 0.036 0.388 19724 Planarity : 0.008 0.141 7764 Dihedral : 13.809 179.182 41685 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.10 % Favored : 97.78 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3287 helix: 0.90 (0.17), residues: 937 sheet: -0.15 (0.19), residues: 697 loop : 0.05 (0.15), residues: 1653 =============================================================================== Job complete usr+sys time: 23657.90 seconds wall clock time: 415 minutes 55.67 seconds (24955.67 seconds total)