Starting phenix.real_space_refine on Thu Dec 7 22:38:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmn_4073/12_2023/5lmn_4073_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmn_4073/12_2023/5lmn_4073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmn_4073/12_2023/5lmn_4073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmn_4073/12_2023/5lmn_4073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmn_4073/12_2023/5lmn_4073_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmn_4073/12_2023/5lmn_4073_neut.pdb" } resolution = 3.55 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1532 5.49 5 Mg 127 5.21 5 S 60 5.16 5 C 27936 2.51 5 N 10188 2.21 5 O 14304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 20": "OE1" <-> "OE2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I GLU 2": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J ASP 73": "OD1" <-> "OD2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "J GLU 97": "OE1" <-> "OE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "M TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O GLU 7": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 83": "OE1" <-> "OE2" Residue "Q GLU 48": "OE1" <-> "OE2" Residue "Q GLU 49": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 78": "OE1" <-> "OE2" Residue "Q GLU 86": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S GLU 21": "OE1" <-> "OE2" Residue "S GLU 43": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "W GLU 15": "OE1" <-> "OE2" Residue "X GLU 73": "OE1" <-> "OE2" Residue "X ARG 91": "NH1" <-> "NH2" Residue "X ARG 123": "NH1" <-> "NH2" Residue "X GLU 126": "OE1" <-> "OE2" Residue "X GLU 131": "OE1" <-> "OE2" Residue "X GLU 134": "OE1" <-> "OE2" Residue "X ARG 139": "NH1" <-> "NH2" Residue "X GLU 142": "OE1" <-> "OE2" Residue "X GLU 155": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 54149 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 32527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1514, 32527 Inner-chain residues flagged as termini: ['pdbres=" G A 567 "'] Classifications: {'RNA': 1514} Modifications used: {'5*END': 2, 'rna2p_pur': 106, 'rna2p_pyr': 79, 'rna3p_pur': 749, 'rna3p_pyr': 579} Link IDs: {'rna2p': 185, 'rna3p': 1328} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1900 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 11, 'TRANS': 222} Chain: "C" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "D" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "E" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1146 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "F" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "G" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1257 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "H" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "I" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 999 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 792 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 892 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "L" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 970 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "M" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 933 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "N" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "O" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "P" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 700 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "Q" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 823 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "R" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 598 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "S" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 647 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "T" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 763 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "V" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 208 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "W" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 570 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "X" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1356 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 160} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 439 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 2} Link IDs: {'rna2p': 5, 'rna3p': 14} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Unusual residues: {' MG': 126} Classifications: {'undetermined': 126} Link IDs: {None: 125} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36098 SG CYS D 9 85.820 103.529 147.785 1.00 25.92 S ATOM 36241 SG CYS D 26 83.109 105.000 147.741 1.00 42.34 S ATOM 36281 SG CYS D 31 84.953 106.919 146.909 1.00 57.10 S ATOM 46881 SG CYS N 24 148.205 114.068 137.058 1.00 45.04 S ATOM 46905 SG CYS N 27 146.059 110.867 136.254 1.00 46.39 S ATOM 47012 SG CYS N 40 147.821 113.126 133.568 1.00 43.14 S ATOM 47037 SG CYS N 43 144.994 114.586 135.557 1.00 40.46 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN N1602 " occ=0.92 Time building chain proxies: 21.69, per 1000 atoms: 0.40 Number of scatterers: 54149 At special positions: 0 Unit cell: (225.12, 179.56, 209.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 60 16.00 P 1532 15.00 Mg 127 11.99 O 14304 8.00 N 10188 7.00 C 27936 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: 24.99 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 300 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 9 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 31 " pdb=" ZN N1602 " pdb="ZN ZN N1602 " - pdb=" SG CYS N 40 " pdb="ZN ZN N1602 " - pdb=" SG CYS N 43 " pdb="ZN ZN N1602 " - pdb=" SG CYS N 24 " pdb="ZN ZN N1602 " - pdb=" SG CYS N 27 " Number of angles added : 6 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4844 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 29 sheets defined 40.5% alpha, 17.8% beta 508 base pairs and 868 stacking pairs defined. Time for finding SS restraints: 21.22 Creating SS restraints... Processing helix chain 'B' and resid 27 through 30 removed outlier: 3.825A pdb=" N ARG B 30 " --> pdb=" O LYS B 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 43 through 63 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.637A pdb=" N ARG B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 122 removed outlier: 3.535A pdb=" N GLN B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 removed outlier: 4.552A pdb=" N LYS B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 180 Processing helix chain 'B' and resid 207 through 227 removed outlier: 3.594A pdb=" N ILE B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.661A pdb=" N VAL B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 240' Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.508A pdb=" N LEU C 32 " --> pdb=" O GLN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.845A pdb=" N VAL C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 108 through 111 removed outlier: 3.674A pdb=" N LEU C 111 " --> pdb=" O ASN C 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 111' Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 145 removed outlier: 3.507A pdb=" N GLY C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.643A pdb=" N ALA C 160 " --> pdb=" O ILE C 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 15 Processing helix chain 'D' and resid 52 through 69 Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 88 through 100 removed outlier: 3.544A pdb=" N ARG D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 149 through 154 removed outlier: 4.432A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 166 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.711A pdb=" N VAL D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 65 Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.804A pdb=" N LEU E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 142 Processing helix chain 'E' and resid 144 through 152 Processing helix chain 'F' and resid 17 through 33 Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 71 through 82 removed outlier: 4.241A pdb=" N ARG F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 53 Processing helix chain 'G' and resid 57 through 70 Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 132 through 147 Processing helix chain 'G' and resid 148 through 154 removed outlier: 4.249A pdb=" N HIS G 153 " --> pdb=" O ALA G 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 19 Processing helix chain 'H' and resid 29 through 43 Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.537A pdb=" N ILE H 100 " --> pdb=" O VAL H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 107 removed outlier: 3.686A pdb=" N ARG H 105 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'I' and resid 33 through 37 Processing helix chain 'I' and resid 42 through 46 Processing helix chain 'I' and resid 47 through 54 removed outlier: 3.645A pdb=" N ARG I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 89 Processing helix chain 'I' and resid 90 through 93 removed outlier: 3.594A pdb=" N ARG I 93 " --> pdb=" O PRO I 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 90 through 93' Processing helix chain 'J' and resid 12 through 29 removed outlier: 3.604A pdb=" N ALA J 18 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 49 Processing helix chain 'K' and resid 53 through 56 Processing helix chain 'K' and resid 57 through 74 Processing helix chain 'K' and resid 89 through 101 removed outlier: 4.571A pdb=" N GLN K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 14 Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.942A pdb=" N TYR M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.521A pdb=" N VAL M 54 " --> pdb=" O GLU M 50 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG M 55 " --> pdb=" O ALA M 51 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.831A pdb=" N ILE M 84 " --> pdb=" O ARG M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 95 Processing helix chain 'M' and resid 107 through 112 Processing helix chain 'N' and resid 3 through 7 Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 Processing helix chain 'O' and resid 50 through 74 removed outlier: 3.529A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 52 through 62 removed outlier: 3.638A pdb=" N ALA P 56 " --> pdb=" O ASP P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 77 Processing helix chain 'Q' and resid 81 through 95 removed outlier: 3.915A pdb=" N VAL Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR Q 95 " --> pdb=" O ARG Q 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 26 removed outlier: 3.618A pdb=" N LEU R 26 " --> pdb=" O VAL R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 57 Processing helix chain 'R' and resid 59 through 77 Processing helix chain 'S' and resid 12 through 25 removed outlier: 4.414A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 45 Processing helix chain 'S' and resid 71 through 75 Processing helix chain 'T' and resid 13 through 47 removed outlier: 3.591A pdb=" N GLU T 46 " --> pdb=" O GLN T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 69 removed outlier: 3.594A pdb=" N GLY T 69 " --> pdb=" O LYS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 94 Processing helix chain 'V' and resid 8 through 15 Processing helix chain 'W' and resid 37 through 43 Processing helix chain 'X' and resid 31 through 42 Processing helix chain 'X' and resid 61 through 79 Processing helix chain 'X' and resid 95 through 113 Processing helix chain 'X' and resid 128 through 144 removed outlier: 3.542A pdb=" N LEU X 132 " --> pdb=" O ALA X 128 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 93 removed outlier: 7.969A pdb=" N VAL B 93 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N PHE B 70 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL B 184 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 60 removed outlier: 3.963A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 63 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASN C 102 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL C 68 " --> pdb=" O GLN C 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 171 Processing sheet with id=AA5, first strand: chain 'D' and resid 126 through 128 removed outlier: 3.663A pdb=" N ASP D 144 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 7 through 20 removed outlier: 5.208A pdb=" N GLU E 8 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY E 35 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N MET E 10 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL E 33 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E 16 " --> pdb=" O ARG E 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 80 through 84 Processing sheet with id=AA8, first strand: chain 'F' and resid 36 through 37 removed outlier: 3.684A pdb=" N GLY F 44 " --> pdb=" O PHE F 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 36 through 37 Processing sheet with id=AB1, first strand: chain 'F' and resid 98 through 99 removed outlier: 3.767A pdb=" N ALA F 99 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE R 29 " --> pdb=" O ALA F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 73 through 79 Processing sheet with id=AB3, first strand: chain 'H' and resid 23 through 27 removed outlier: 3.761A pdb=" N GLY H 47 " --> pdb=" O TYR H 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AB5, first strand: chain 'H' and resid 83 through 85 Processing sheet with id=AB6, first strand: chain 'H' and resid 83 through 85 removed outlier: 4.917A pdb=" N LEU H 133 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N SER H 113 " --> pdb=" O LEU H 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 6 removed outlier: 5.963A pdb=" N THR I 27 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL I 65 " --> pdb=" O THR I 27 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 38 through 43 removed outlier: 4.058A pdb=" N ASN J 69 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR J 42 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N THR J 67 " --> pdb=" O THR J 42 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 47 through 50 removed outlier: 3.890A pdb=" N VAL J 49 " --> pdb=" O GLU J 61 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 39 through 43 removed outlier: 6.061A pdb=" N ALA K 19 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG K 85 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE K 21 " --> pdb=" O ARG K 85 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL K 80 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE K 108 " --> pdb=" O VAL K 80 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL K 82 " --> pdb=" O ILE K 108 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP K 110 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL K 84 " --> pdb=" O ASP K 110 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 82 through 84 removed outlier: 6.478A pdb=" N LYS L 57 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL L 40 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL L 55 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR L 42 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG L 53 " --> pdb=" O THR L 42 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR L 98 " --> pdb=" O THR L 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 34 through 35 Processing sheet with id=AC5, first strand: chain 'P' and resid 37 through 39 Processing sheet with id=AC6, first strand: chain 'Q' and resid 5 through 15 removed outlier: 6.950A pdb=" N GLY Q 8 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLU Q 24 " --> pdb=" O GLY Q 8 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL Q 10 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU Q 22 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS Q 14 " --> pdb=" O THR Q 18 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR Q 18 " --> pdb=" O LYS Q 14 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG Q 38 " --> pdb=" O ARG Q 25 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE Q 71 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU Q 76 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL Q 56 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 31 through 33 Processing sheet with id=AC8, first strand: chain 'W' and resid 10 through 17 removed outlier: 5.335A pdb=" N VAL W 13 " --> pdb=" O LYS W 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS W 25 " --> pdb=" O VAL W 13 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR W 21 " --> pdb=" O LEU W 17 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE W 32 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N GLY W 65 " --> pdb=" O GLU W 31 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU W 33 " --> pdb=" O GLY W 65 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE W 67 " --> pdb=" O LEU W 33 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR W 35 " --> pdb=" O ILE W 67 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N TYR W 69 " --> pdb=" O TYR W 35 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL W 54 " --> pdb=" O VAL W 68 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 27 through 30 removed outlier: 3.720A pdb=" N GLY X 27 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ALA X 57 " --> pdb=" O GLN X 15 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARG X 17 " --> pdb=" O ALA X 57 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE X 59 " --> pdb=" O ARG X 17 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL X 19 " --> pdb=" O ILE X 59 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG X 58 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU X 47 " --> pdb=" O ARG X 58 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N MET X 60 " --> pdb=" O LEU X 45 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU X 45 " --> pdb=" O MET X 60 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 85 through 87 Processing sheet with id=AD2, first strand: chain 'X' and resid 120 through 121 946 hydrogen bonds defined for protein. 2703 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1353 hydrogen bonds 2290 hydrogen bond angles 0 basepair planarities 508 basepair parallelities 868 stacking parallelities Total time for adding SS restraints: 47.72 Time building geometry restraints manager: 26.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6986 1.33 - 1.45: 24769 1.45 - 1.58: 23432 1.58 - 1.71: 2991 1.71 - 1.83: 107 Bond restraints: 58285 Sorted by residual: bond pdb=" O3' C A1459 " pdb=" P A A1460 " ideal model delta sigma weight residual 1.607 1.505 0.102 1.50e-02 4.44e+03 4.66e+01 bond pdb=" O3' G A1458 " pdb=" P C A1459 " ideal model delta sigma weight residual 1.607 1.697 -0.090 1.50e-02 4.44e+03 3.61e+01 bond pdb=" O3' C A 999 " pdb=" P U A1000 " ideal model delta sigma weight residual 1.607 1.539 0.068 1.50e-02 4.44e+03 2.04e+01 bond pdb=" O3' A A 559 " pdb=" P U A 560 " ideal model delta sigma weight residual 1.607 1.671 -0.064 1.50e-02 4.44e+03 1.80e+01 bond pdb=" O3' G A 79 " pdb=" P G A 80 " ideal model delta sigma weight residual 1.607 1.545 0.062 1.50e-02 4.44e+03 1.71e+01 ... (remaining 58280 not shown) Histogram of bond angle deviations from ideal: 53.24 - 69.54: 2 69.54 - 85.84: 0 85.84 - 102.14: 2388 102.14 - 118.44: 52223 118.44 - 134.74: 31658 Bond angle restraints: 86271 Sorted by residual: angle pdb=" O3' G A 93 " pdb=" P U A 96 " pdb=" O5' U A 96 " ideal model delta sigma weight residual 104.00 53.24 50.76 1.50e+00 4.44e-01 1.15e+03 angle pdb=" O3' G A 93 " pdb=" P U A 96 " pdb=" OP1 U A 96 " ideal model delta sigma weight residual 108.00 56.43 51.57 3.00e+00 1.11e-01 2.95e+02 angle pdb=" N ILE C 14 " pdb=" CA ILE C 14 " pdb=" C ILE C 14 " ideal model delta sigma weight residual 111.62 122.82 -11.20 7.90e-01 1.60e+00 2.01e+02 angle pdb=" C4' A A1001 " pdb=" C3' A A1001 " pdb=" O3' A A1001 " ideal model delta sigma weight residual 113.00 92.24 20.76 1.50e+00 4.44e-01 1.91e+02 angle pdb=" O3' G A 266 " pdb=" C3' G A 266 " pdb=" C2' G A 266 " ideal model delta sigma weight residual 109.50 128.07 -18.57 1.50e+00 4.44e-01 1.53e+02 ... (remaining 86266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 31576 35.99 - 71.97: 4498 71.97 - 107.96: 590 107.96 - 143.95: 22 143.95 - 179.93: 45 Dihedral angle restraints: 36731 sinusoidal: 29196 harmonic: 7535 Sorted by residual: dihedral pdb=" C5' C A1145 " pdb=" C4' C A1145 " pdb=" C3' C A1145 " pdb=" O3' C A1145 " ideal model delta sinusoidal sigma weight residual 147.00 73.42 73.58 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" C5' G A1504 " pdb=" C4' G A1504 " pdb=" C3' G A1504 " pdb=" O3' G A1504 " ideal model delta sinusoidal sigma weight residual 147.00 73.47 73.53 1 8.00e+00 1.56e-02 1.07e+02 dihedral pdb=" C5' C A 840 " pdb=" C4' C A 840 " pdb=" C3' C A 840 " pdb=" O3' C A 840 " ideal model delta sinusoidal sigma weight residual 147.00 76.99 70.01 1 8.00e+00 1.56e-02 9.87e+01 ... (remaining 36728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.236: 10301 0.236 - 0.471: 473 0.471 - 0.707: 22 0.707 - 0.943: 10 0.943 - 1.178: 2 Chirality restraints: 10808 Sorted by residual: chirality pdb=" C3' G A 115 " pdb=" C4' G A 115 " pdb=" O3' G A 115 " pdb=" C2' G A 115 " both_signs ideal model delta sigma weight residual False -2.74 -1.57 -1.18 2.00e-01 2.50e+01 3.47e+01 chirality pdb=" C3' U A1498 " pdb=" C4' U A1498 " pdb=" O3' U A1498 " pdb=" C2' U A1498 " both_signs ideal model delta sigma weight residual False -2.74 -1.69 -1.06 2.00e-01 2.50e+01 2.80e+01 chirality pdb=" C3' G A 181 " pdb=" C4' G A 181 " pdb=" O3' G A 181 " pdb=" C2' G A 181 " both_signs ideal model delta sigma weight residual False -2.74 -1.86 -0.89 2.00e-01 2.50e+01 1.98e+01 ... (remaining 10805 not shown) Planarity restraints: 5246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1458 " 0.051 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" N9 G A1458 " 0.006 2.00e-02 2.50e+03 pdb=" C8 G A1458 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A1458 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A1458 " -0.052 2.00e-02 2.50e+03 pdb=" C6 G A1458 " -0.093 2.00e-02 2.50e+03 pdb=" O6 G A1458 " 0.131 2.00e-02 2.50e+03 pdb=" N1 G A1458 " -0.022 2.00e-02 2.50e+03 pdb=" C2 G A1458 " -0.080 2.00e-02 2.50e+03 pdb=" N2 G A1458 " 0.075 2.00e-02 2.50e+03 pdb=" N3 G A1458 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A1458 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 76 " 0.044 2.00e-02 2.50e+03 5.59e-02 7.04e+01 pdb=" N1 C A 76 " -0.009 2.00e-02 2.50e+03 pdb=" C2 C A 76 " -0.118 2.00e-02 2.50e+03 pdb=" O2 C A 76 " 0.070 2.00e-02 2.50e+03 pdb=" N3 C A 76 " -0.015 2.00e-02 2.50e+03 pdb=" C4 C A 76 " -0.044 2.00e-02 2.50e+03 pdb=" N4 C A 76 " 0.071 2.00e-02 2.50e+03 pdb=" C5 C A 76 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C A 76 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 70 " -0.011 2.00e-02 2.50e+03 4.82e-02 6.98e+01 pdb=" N9 G A 70 " -0.007 2.00e-02 2.50e+03 pdb=" C8 G A 70 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G A 70 " 0.017 2.00e-02 2.50e+03 pdb=" C5 G A 70 " 0.014 2.00e-02 2.50e+03 pdb=" C6 G A 70 " -0.103 2.00e-02 2.50e+03 pdb=" O6 G A 70 " 0.064 2.00e-02 2.50e+03 pdb=" N1 G A 70 " -0.023 2.00e-02 2.50e+03 pdb=" C2 G A 70 " -0.070 2.00e-02 2.50e+03 pdb=" N2 G A 70 " 0.075 2.00e-02 2.50e+03 pdb=" N3 G A 70 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 70 " 0.038 2.00e-02 2.50e+03 ... (remaining 5243 not shown) Histogram of nonbonded interaction distances: 0.93 - 1.72: 21 1.72 - 2.52: 302 2.52 - 3.31: 62438 3.31 - 4.10: 188045 4.10 - 4.90: 266197 Warning: very small nonbonded interaction distances. Nonbonded interactions: 517003 Sorted by model distance: nonbonded pdb=" CD1 LEU B 10 " pdb=" SD MET B 48 " model vdw 0.925 3.820 nonbonded pdb=" CG ARG N 23 " pdb=" O ARG N 29 " model vdw 1.162 3.440 nonbonded pdb=" O LYS J 57 " pdb=" NH2 ARG J 60 " model vdw 1.302 2.520 nonbonded pdb=" NZ LYS J 57 " pdb=" NH1 ARG J 60 " model vdw 1.414 3.200 nonbonded pdb=" CD1 LEU B 10 " pdb=" CG MET B 48 " model vdw 1.419 3.860 ... (remaining 516998 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=0.92 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.030 Extract box with map and model: 6.070 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 166.050 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.150 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:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 : 0.007 0.102 58285 Z= 0.452 Angle : 1.421 51.570 86271 Z= 0.947 Chirality : 0.116 1.178 10808 Planarity : 0.010 0.184 5246 Dihedral : 26.100 179.933 31887 Min Nonbonded Distance : 0.925 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 2.83 % Allowed : 10.43 % Favored : 86.74 % Rotamer: Outliers : 21.59 % Allowed : 19.32 % Favored : 59.09 % Cbeta Deviations : 1.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.30 (0.15), residues: 2579 helix: 0.34 (0.14), residues: 1004 sheet: -2.10 (0.22), residues: 423 loop : -3.10 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP P 59 HIS 0.014 0.002 HIS D 43 PHE 0.029 0.003 PHE O 15 TYR 0.028 0.003 TYR D 4 ARG 0.026 0.002 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1462 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 474 poor density : 988 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 474 outliers final: 124 residues processed: 1233 average time/residue: 0.7111 time to fit residues: 1369.6796 Evaluate side-chains 878 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 754 time to evaluate : 2.689 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 2 residues processed: 124 average time/residue: 0.5709 time to fit residues: 120.5583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 341 optimal weight: 0.4980 chunk 306 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 163 optimal weight: 20.0000 chunk 317 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 chunk 367 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 146 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN D 160 GLN E 56 GLN E 72 GLN E 73 ASN E 141 GLN F 64 GLN F 100 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 HIS K 116 HIS L 75 HIS O 37 ASN Q 45 HIS S 53 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 58285 Z= 0.248 Angle : 0.777 15.674 86271 Z= 0.395 Chirality : 0.042 0.375 10808 Planarity : 0.006 0.064 5246 Dihedral : 24.733 179.612 26413 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.68 % Favored : 91.74 % Rotamer: Outliers : 5.65 % Allowed : 29.16 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.16), residues: 2579 helix: 1.70 (0.17), residues: 1000 sheet: -1.65 (0.23), residues: 443 loop : -2.52 (0.16), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 167 HIS 0.008 0.001 HIS D 43 PHE 0.025 0.002 PHE X 109 TYR 0.022 0.002 TYR C 29 ARG 0.009 0.001 ARG F 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 872 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 47 residues processed: 941 average time/residue: 0.5866 time to fit residues: 891.1172 Evaluate side-chains 760 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 713 time to evaluate : 2.753 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 47 outliers final: 1 residues processed: 47 average time/residue: 0.4215 time to fit residues: 39.7517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 204 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 306 optimal weight: 6.9990 chunk 250 optimal weight: 0.0570 chunk 101 optimal weight: 30.0000 chunk 368 optimal weight: 7.9990 chunk 398 optimal weight: 10.0000 chunk 328 optimal weight: 6.9990 chunk 365 optimal weight: 0.7980 chunk 125 optimal weight: 20.0000 chunk 295 optimal weight: 5.9990 overall best weight: 3.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 HIS ** B 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 181 ASN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS E 130 ASN E 141 GLN F 13 ASN F 64 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN O 71 GLN Q 45 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 58285 Z= 0.248 Angle : 0.692 14.734 86271 Z= 0.351 Chirality : 0.038 0.289 10808 Planarity : 0.005 0.060 5246 Dihedral : 24.283 177.760 26413 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.56 % Favored : 91.97 % Rotamer: Outliers : 5.79 % Allowed : 29.79 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.92 (0.16), residues: 2579 helix: 1.38 (0.16), residues: 1014 sheet: -1.54 (0.23), residues: 449 loop : -2.14 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 24 HIS 0.009 0.001 HIS I 58 PHE 0.025 0.002 PHE X 109 TYR 0.028 0.002 TYR M 23 ARG 0.007 0.001 ARG Q 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 821 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 65 residues processed: 881 average time/residue: 0.5872 time to fit residues: 845.2475 Evaluate side-chains 775 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 710 time to evaluate : 2.701 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.4193 time to fit residues: 54.3229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 364 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 247 optimal weight: 20.0000 chunk 369 optimal weight: 6.9990 chunk 391 optimal weight: 0.7980 chunk 193 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN E 141 GLN F 13 ASN F 57 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN G 96 GLN G 97 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS K 13 GLN K 93 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 58285 Z= 0.302 Angle : 0.703 15.143 86271 Z= 0.355 Chirality : 0.039 0.293 10808 Planarity : 0.005 0.060 5246 Dihedral : 24.149 179.416 26413 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.86 % Favored : 92.67 % Rotamer: Outliers : 4.97 % Allowed : 31.39 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.97 (0.16), residues: 2579 helix: 1.15 (0.16), residues: 1010 sheet: -1.43 (0.24), residues: 434 loop : -2.02 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 24 HIS 0.006 0.001 HIS I 58 PHE 0.034 0.003 PHE C 10 TYR 0.018 0.002 TYR D 4 ARG 0.006 0.001 ARG O 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 757 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 57 residues processed: 809 average time/residue: 0.5618 time to fit residues: 747.3256 Evaluate side-chains 759 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 702 time to evaluate : 2.713 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.4524 time to fit residues: 49.8927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 326 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 291 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 334 optimal weight: 0.9990 chunk 270 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 351 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN C 6 HIS ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN D 123 HIS D 154 ASN E 38 GLN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS J 56 HIS J 84 GLN K 13 GLN K 93 GLN ** L 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 58285 Z= 0.196 Angle : 0.641 14.461 86271 Z= 0.322 Chirality : 0.036 0.309 10808 Planarity : 0.005 0.054 5246 Dihedral : 24.003 177.600 26413 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.90 % Favored : 92.75 % Rotamer: Outliers : 3.05 % Allowed : 33.30 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.16), residues: 2579 helix: 1.20 (0.16), residues: 1003 sheet: -1.33 (0.24), residues: 435 loop : -1.90 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 24 HIS 0.007 0.001 HIS I 58 PHE 0.027 0.002 PHE C 10 TYR 0.036 0.002 TYR M 23 ARG 0.005 0.000 ARG O 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 752 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 34 residues processed: 777 average time/residue: 0.5772 time to fit residues: 734.9773 Evaluate side-chains 735 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 701 time to evaluate : 2.711 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4273 time to fit residues: 29.6445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 131 optimal weight: 10.0000 chunk 352 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 391 optimal weight: 30.0000 chunk 325 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN F 18 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS I 124 GLN J 84 GLN K 93 GLN L 49 ASN M 12 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 58285 Z= 0.388 Angle : 0.752 15.873 86271 Z= 0.377 Chirality : 0.040 0.300 10808 Planarity : 0.005 0.060 5246 Dihedral : 24.046 179.834 26413 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.91 % Favored : 91.82 % Rotamer: Outliers : 4.15 % Allowed : 33.58 % Favored : 62.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2579 helix: 0.74 (0.16), residues: 1021 sheet: -1.45 (0.23), residues: 437 loop : -1.92 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 24 HIS 0.007 0.001 HIS I 58 PHE 0.030 0.003 PHE C 10 TYR 0.020 0.002 TYR D 4 ARG 0.007 0.001 ARG L 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 723 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 50 residues processed: 761 average time/residue: 0.5876 time to fit residues: 732.5207 Evaluate side-chains 718 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 668 time to evaluate : 2.695 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.4527 time to fit residues: 43.7703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 377 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 221 optimal weight: 0.7980 chunk 329 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 390 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN D 154 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS J 84 GLN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN L 8 ASN ** L 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 ASN X 15 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 58285 Z= 0.290 Angle : 0.700 15.233 86271 Z= 0.352 Chirality : 0.038 0.387 10808 Planarity : 0.005 0.069 5246 Dihedral : 24.020 179.231 26413 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.87 % Favored : 91.86 % Rotamer: Outliers : 2.41 % Allowed : 34.72 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.16), residues: 2579 helix: 0.68 (0.16), residues: 1018 sheet: -1.41 (0.23), residues: 440 loop : -1.90 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 24 HIS 0.008 0.001 HIS I 58 PHE 0.030 0.002 PHE C 10 TYR 0.021 0.002 TYR I 88 ARG 0.006 0.001 ARG H 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 694 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 29 residues processed: 720 average time/residue: 0.5915 time to fit residues: 703.1179 Evaluate side-chains 678 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 649 time to evaluate : 2.859 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4200 time to fit residues: 25.6890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 241 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 233 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 162 GLN D 103 ASN D 154 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN ** I 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS J 84 GLN K 93 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN L 49 ASN L 76 ASN M 12 ASN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 58285 Z= 0.358 Angle : 0.745 15.613 86271 Z= 0.374 Chirality : 0.040 0.287 10808 Planarity : 0.005 0.068 5246 Dihedral : 24.030 179.968 26413 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.45 % Favored : 91.28 % Rotamer: Outliers : 2.37 % Allowed : 36.04 % Favored : 61.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.16), residues: 2579 helix: 0.44 (0.16), residues: 1024 sheet: -1.42 (0.23), residues: 442 loop : -1.95 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 24 HIS 0.008 0.001 HIS I 58 PHE 0.028 0.003 PHE C 10 TYR 0.031 0.002 TYR D 4 ARG 0.007 0.001 ARG W 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 670 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 31 residues processed: 693 average time/residue: 0.5748 time to fit residues: 654.7353 Evaluate side-chains 672 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 641 time to evaluate : 2.712 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4665 time to fit residues: 28.5792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 355 optimal weight: 8.9990 chunk 373 optimal weight: 9.9990 chunk 341 optimal weight: 0.7980 chunk 363 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 328 optimal weight: 2.9990 chunk 344 optimal weight: 0.8980 chunk 362 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 135 GLN C 162 GLN D 154 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS J 84 GLN L 8 ASN M 12 ASN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 58285 Z= 0.184 Angle : 0.653 14.524 86271 Z= 0.328 Chirality : 0.036 0.311 10808 Planarity : 0.005 0.064 5246 Dihedral : 23.922 179.723 26413 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.98 % Favored : 92.75 % Rotamer: Outliers : 1.23 % Allowed : 36.63 % Favored : 62.14 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.16), residues: 2579 helix: 0.67 (0.16), residues: 1018 sheet: -1.15 (0.24), residues: 424 loop : -1.80 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 24 HIS 0.009 0.001 HIS I 58 PHE 0.029 0.002 PHE C 10 TYR 0.025 0.001 TYR I 88 ARG 0.007 0.000 ARG W 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 694 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 708 average time/residue: 0.5795 time to fit residues: 675.5704 Evaluate side-chains 673 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 659 time to evaluate : 2.733 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5912 time to fit residues: 16.6358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 238 optimal weight: 0.0470 chunk 384 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 267 optimal weight: 6.9990 chunk 403 optimal weight: 40.0000 chunk 371 optimal weight: 9.9990 chunk 321 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 HIS C 107 GLN D 154 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 ASN M 101 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 58285 Z= 0.240 Angle : 0.677 15.101 86271 Z= 0.339 Chirality : 0.036 0.321 10808 Planarity : 0.005 0.067 5246 Dihedral : 23.892 179.320 26413 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.44 % Favored : 92.25 % Rotamer: Outliers : 0.96 % Allowed : 37.72 % Favored : 61.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.16), residues: 2579 helix: 0.69 (0.16), residues: 1004 sheet: -1.28 (0.24), residues: 449 loop : -1.79 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 24 HIS 0.009 0.001 HIS I 58 PHE 0.033 0.002 PHE D 206 TYR 0.026 0.002 TYR D 4 ARG 0.008 0.001 ARG H 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 673 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 681 average time/residue: 0.5686 time to fit residues: 641.0778 Evaluate side-chains 662 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 648 time to evaluate : 2.751 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4691 time to fit residues: 14.4945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 255 optimal weight: 6.9990 chunk 342 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 296 optimal weight: 0.1980 chunk 47 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 321 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 330 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 GLN D 154 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 ASN I 58 HIS ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN M 12 ASN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.097671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.079032 restraints weight = 149110.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.081450 restraints weight = 72592.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.081351 restraints weight = 38194.089| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 58285 Z= 0.298 Angle : 0.710 15.493 86271 Z= 0.357 Chirality : 0.038 0.316 10808 Planarity : 0.005 0.064 5246 Dihedral : 23.919 179.509 26413 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.07 % Favored : 91.66 % Rotamer: Outliers : 1.05 % Allowed : 38.04 % Favored : 60.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.16), residues: 2579 helix: 0.60 (0.16), residues: 993 sheet: -1.29 (0.24), residues: 445 loop : -1.76 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 24 HIS 0.008 0.001 HIS I 58 PHE 0.033 0.003 PHE D 206 TYR 0.026 0.002 TYR D 4 ARG 0.009 0.001 ARG O 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11910.91 seconds wall clock time: 210 minutes 58.12 seconds (12658.12 seconds total)