Starting phenix.real_space_refine on Mon Nov 13 21:49:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmo_4074/11_2023/5lmo_4074_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmo_4074/11_2023/5lmo_4074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmo_4074/11_2023/5lmo_4074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmo_4074/11_2023/5lmo_4074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmo_4074/11_2023/5lmo_4074_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmo_4074/11_2023/5lmo_4074_neut.pdb" } resolution = 4.3 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= 0.017 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 1530 5.49 5 Mg 108 5.21 5 S 60 5.16 5 C 27927 2.51 5 N 10186 2.21 5 O 14297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 9": "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 119": "OE1" <-> "OE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D GLU 60": "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 163": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "F GLU 69": "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 22": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H ARG 105": "NH1" <-> "NH2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I GLU 2": "OE1" <-> "OE2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "K TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 16": "OE1" <-> "OE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "M TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 83": "OE1" <-> "OE2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 78": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 38": "OE1" <-> "OE2" Residue "R GLU 62": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T GLU 93": "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 159": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 54110 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 32525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1514, 32525 Inner-chain residues flagged as termini: ['pdbres=" G A 567 "', 'pdbres=" C A1397 "'] Classifications: {'RNA': 1514} Modifications used: {'5*END': 3, 'rna2p_pur': 107, 'rna2p_pyr': 75, 'rna3p_pur': 748, 'rna3p_pyr': 584} Link IDs: {'rna2p': 182, 'rna3p': 1331} Chain breaks: 7 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: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} 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: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 885 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} 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} Chain breaks: 2 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: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 288 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 2} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 174 Unusual residues: {' MG': 107} Classifications: {'RNA': 3, 'undetermined': 107} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'MG-O1P': 1, 'rna2p': 1, 'rna3p': 1, None: 106} Not linked: pdbres=" MG A1601 " pdbres=" MG A1602 " Not linked: pdbres=" MG A1602 " pdbres=" MG A1603 " Not linked: pdbres=" MG A1603 " pdbres=" MG A1604 " Not linked: pdbres=" MG A1604 " pdbres=" MG A1605 " Not linked: pdbres=" MG A1605 " pdbres=" MG A1606 " ... (remaining 101 not shown) Chain breaks: 2 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {' MG': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p_pyr': 1} Link IDs: {'MG-O1P': 1} Chain breaks: 1 Chain: "X" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36096 SG CYS D 9 86.848 103.102 148.002 1.00 50.00 S ATOM 36239 SG CYS D 26 84.159 104.697 147.884 1.00 50.00 S ATOM 36279 SG CYS D 31 86.312 106.296 147.052 1.00 50.00 S ATOM 46883 SG CYS N 24 153.263 114.450 136.047 1.00 50.00 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="ZN ZN N 101 " occ=0.92 residue: pdb="MG MG W 101 " occ=0.63 Time building chain proxies: 20.41, per 1000 atoms: 0.38 Number of scatterers: 54110 At special positions: 0 Unit cell: (229.14, 179.56, 206.36, 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 1530 15.00 Mg 108 11.99 O 14297 8.00 N 10186 7.00 C 27927 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 Atom "ATOM 20318 O5' C A 972 .*. O " rejected from bonding due to valence issues. Atom "ATOM 20318 O5' C A 972 .*. O " rejected from bonding due to valence issues. Atom "ATOM 20318 O5' C A 972 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 23.84 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 300 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 9 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 31 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4842 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 26 sheets defined 38.2% alpha, 19.6% beta 502 base pairs and 865 stacking pairs defined. Time for finding SS restraints: 19.33 Creating SS restraints... Processing helix chain 'B' and resid 43 through 66 removed outlier: 3.831A pdb=" N GLY B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 88 removed outlier: 3.621A pdb=" N GLU B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 119 removed outlier: 3.766A pdb=" N ARG B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.608A pdb=" N GLU B 128 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 149 removed outlier: 3.564A pdb=" N TYR B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 180 removed outlier: 3.518A pdb=" N VAL B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 227 removed outlier: 3.755A pdb=" N ILE B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 12 removed outlier: 3.635A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.966A pdb=" N LEU C 32 " --> pdb=" O GLN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 82 through 95 removed outlier: 3.808A pdb=" N VAL C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 87 " --> pdb=" O ARG C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 127 Processing helix chain 'C' and resid 129 through 144 Processing helix chain 'C' and resid 177 through 180 Processing helix chain 'D' and resid 8 through 16 removed outlier: 3.756A pdb=" N CYS D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.536A pdb=" N GLN D 45 " --> pdb=" O GLN D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 69 removed outlier: 3.730A pdb=" N ARG D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 113 through 124 removed outlier: 3.810A pdb=" N GLY D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 165 Processing helix chain 'D' and resid 200 through 209 removed outlier: 4.072A pdb=" N ARG D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 65 Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.851A pdb=" N ALA E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE E 109 " --> pdb=" O VAL E 105 " (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 16 through 33 removed outlier: 3.793A pdb=" N ALA F 20 " --> pdb=" O GLN F 16 " (cutoff:3.500A) 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: 4.216A pdb=" N ARG F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.852A pdb=" N THR G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 53 removed outlier: 3.570A pdb=" N ARG G 41 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 70 Processing helix chain 'G' and resid 92 through 110 Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 133 through 148 removed outlier: 3.672A pdb=" N ASN G 148 " --> pdb=" O MET G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 152 removed outlier: 3.744A pdb=" N ALA G 152 " --> pdb=" O ARG G 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 149 through 152' Processing helix chain 'H' and resid 4 through 20 removed outlier: 3.752A pdb=" N ASP H 8 " --> pdb=" O ASP H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 43 Processing helix chain 'H' and resid 102 through 107 removed outlier: 3.534A 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 40 through 46 removed outlier: 3.574A pdb=" N ALA I 43 " --> pdb=" O LEU I 40 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL I 44 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA I 45 " --> pdb=" O ARG I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 54 removed outlier: 3.654A pdb=" N ALA I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL I 53 " --> pdb=" O PRO I 49 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 48 through 54' Processing helix chain 'I' and resid 69 through 89 Processing helix chain 'I' and resid 91 through 95 Processing helix chain 'J' and resid 12 through 20 Processing helix chain 'K' and resid 45 through 49 Processing helix chain 'K' and resid 52 through 57 removed outlier: 4.015A pdb=" N GLY K 56 " --> pdb=" O GLY K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 74 Processing helix chain 'K' and resid 90 through 101 Processing helix chain 'L' and resid 6 through 13 Processing helix chain 'L' and resid 117 through 121 Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.578A pdb=" N TYR M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 removed outlier: 3.647A pdb=" N LYS M 31 " --> pdb=" O LYS M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.501A pdb=" N VAL M 53 " --> pdb=" O THR M 49 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG M 55 " --> pdb=" O ALA M 51 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU M 56 " --> pdb=" O GLU M 52 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 84 removed outlier: 3.502A pdb=" N ARG M 71 " --> pdb=" O GLU M 67 " (cutoff:3.500A) removed outlier: 3.746A 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 40 through 51 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 4.145A pdb=" N VAL O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS O 46 " --> pdb=" O HIS O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 74 Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 67 through 78 Processing helix chain 'Q' and resid 81 through 99 removed outlier: 3.971A pdb=" N VAL Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER Q 99 " --> pdb=" O TYR Q 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 57 removed outlier: 3.519A pdb=" N GLY R 57 " --> pdb=" O ARG R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 77 Processing helix chain 'S' and resid 71 through 75 removed outlier: 3.880A pdb=" N PHE S 74 " --> pdb=" O LEU S 71 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA S 75 " --> pdb=" O GLY S 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 71 through 75' Processing helix chain 'T' and resid 12 through 46 removed outlier: 3.862A pdb=" N HIS T 16 " --> pdb=" O ALA T 12 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU T 46 " --> pdb=" O GLN T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 69 removed outlier: 3.511A pdb=" N GLY T 69 " --> pdb=" O LYS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 92 removed outlier: 3.696A pdb=" N ALA T 78 " --> pdb=" O LYS T 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 16 Processing helix chain 'W' and resid 37 through 44 Processing helix chain 'X' and resid 31 through 42 Processing helix chain 'X' and resid 61 through 77 Processing helix chain 'X' and resid 95 through 113 Processing helix chain 'X' and resid 128 through 144 removed outlier: 3.781A 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 removed outlier: 7.162A pdb=" N ILE B 41 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ILE B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 68 through 71 Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 21 removed outlier: 4.009A pdb=" N ARG C 59 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS C 69 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N THR C 67 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE C 57 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 171 removed outlier: 3.829A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 154 " --> pdb=" O GLY C 197 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY C 197 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AA6, first strand: chain 'E' and resid 7 through 16 removed outlier: 5.427A pdb=" N GLU E 8 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY E 35 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N MET E 10 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL E 33 " --> pdb=" O MET E 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AA8, first strand: chain 'E' and resid 80 through 84 removed outlier: 3.550A pdb=" N PHE E 84 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 36 through 47 removed outlier: 7.052A pdb=" N GLU F 38 " --> pdb=" O GLU F 66 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N GLU F 66 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL F 40 " --> pdb=" O GLN F 64 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLN F 64 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU F 42 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP F 62 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY F 44 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY F 58 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ARG F 3 " --> pdb=" O LYS F 92 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LYS F 92 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU F 5 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN F 7 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL F 88 " --> pdb=" O ASN F 7 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL F 9 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 98 through 99 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: 3.521A pdb=" N THR H 24 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU H 49 " --> pdb=" O ARG H 60 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 82 through 85 Processing sheet with id=AB5, first strand: chain 'H' and resid 82 through 85 removed outlier: 5.720A pdb=" N LEU H 133 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER H 113 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS H 135 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU H 119 " --> pdb=" O LEU H 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 4 through 10 removed outlier: 3.607A pdb=" N GLY I 8 " --> pdb=" O ALA I 15 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LYS I 25 " --> pdb=" O ALA I 61 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE I 63 " --> pdb=" O LYS I 25 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N THR I 27 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL I 65 " --> pdb=" O THR I 27 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 39 through 48 removed outlier: 5.765A pdb=" N LEU J 71 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASN J 69 " --> pdb=" O PRO J 41 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL J 72 " --> pdb=" O ILE J 6 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 39 through 48 removed outlier: 5.765A pdb=" N LEU J 71 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASN J 69 " --> pdb=" O PRO J 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 41 through 43 removed outlier: 7.954A pdb=" N VAL K 80 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE K 108 " --> pdb=" O VAL K 80 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL K 82 " --> pdb=" O ILE K 108 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASP K 110 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL K 84 " --> pdb=" O ASP K 110 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU R 85 " --> pdb=" O ASP K 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 82 through 85 removed outlier: 4.999A pdb=" N CYS L 37 " --> pdb=" O ARG L 59 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG L 59 " --> pdb=" O CYS L 37 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL L 39 " --> pdb=" O LYS L 57 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR L 98 " --> pdb=" O THR L 67 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 50 through 51 removed outlier: 5.439A pdb=" N LYS P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL P 21 " --> pdb=" O LYS P 35 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Q' and resid 5 through 12 removed outlier: 12.628A pdb=" N LEU Q 6 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.662A pdb=" N GLN Q 26 " --> pdb=" O LEU Q 6 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLY Q 8 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLU Q 24 " --> pdb=" O GLY Q 8 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL Q 10 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU Q 22 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER Q 12 " --> pdb=" O THR Q 20 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS Q 69 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU Q 43 " --> pdb=" O LYS Q 69 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE Q 71 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG Q 70 " --> pdb=" O SER Q 62 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU Q 76 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL Q 56 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 31 through 33 Processing sheet with id=AC5, first strand: chain 'W' and resid 7 through 16 removed outlier: 6.233A pdb=" N ARG W 23 " --> pdb=" O THR W 14 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA W 16 " --> pdb=" O THR W 21 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR W 21 " --> pdb=" O ALA W 16 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL W 24 " --> pdb=" O ILE W 32 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE W 32 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ILE W 67 " --> pdb=" O LEU W 33 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR W 35 " --> pdb=" O ILE W 67 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG W 66 " --> pdb=" O GLU W 56 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 25 through 30 removed outlier: 3.567A pdb=" N GLY X 27 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA X 57 " --> pdb=" O GLN X 15 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG X 17 " --> pdb=" O ALA X 57 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE X 59 " --> pdb=" O ARG X 17 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL X 19 " --> pdb=" O ILE X 59 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL X 56 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 85 through 90 removed outlier: 3.789A pdb=" N MET X 121 " --> pdb=" O PHE X 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 85 through 90 removed outlier: 3.789A pdb=" N MET X 121 " --> pdb=" O PHE X 90 " (cutoff:3.500A) 921 hydrogen bonds defined for protein. 2631 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1340 hydrogen bonds 2274 hydrogen bond angles 0 basepair planarities 502 basepair parallelities 865 stacking parallelities Total time for adding SS restraints: 42.19 Time building geometry restraints manager: 25.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.50: 39894 1.50 - 1.79: 18252 1.79 - 2.08: 106 2.08 - 2.36: 0 2.36 - 2.65: 1 Bond restraints: 58253 Sorted by residual: bond pdb=" O3' G A 927 " pdb=" P G A 928 " ideal model delta sigma weight residual 1.607 2.653 -1.046 1.50e-02 4.44e+03 4.86e+03 bond pdb=" N ARG R 18 " pdb=" CA ARG R 18 " ideal model delta sigma weight residual 1.457 1.514 -0.056 1.29e-02 6.01e+03 1.89e+01 bond pdb=" CA PRO G 58 " pdb=" C PRO G 58 " ideal model delta sigma weight residual 1.520 1.561 -0.041 9.50e-03 1.11e+04 1.87e+01 bond pdb=" N VAL S 67 " pdb=" CA VAL S 67 " ideal model delta sigma weight residual 1.456 1.497 -0.040 9.50e-03 1.11e+04 1.81e+01 bond pdb=" CA THR K 57 " pdb=" C THR K 57 " ideal model delta sigma weight residual 1.528 1.571 -0.043 1.01e-02 9.80e+03 1.81e+01 ... (remaining 58248 not shown) Histogram of bond angle deviations from ideal: 79.83 - 94.42: 4 94.42 - 109.01: 19037 109.01 - 123.61: 57215 123.61 - 138.20: 9942 138.20 - 152.79: 2 Bond angle restraints: 86200 Sorted by residual: angle pdb=" O3' G A 927 " pdb=" P G A 928 " pdb=" O5' G A 928 " ideal model delta sigma weight residual 104.00 152.15 -48.15 1.50e+00 4.44e-01 1.03e+03 angle pdb=" C LYS I 11 " pdb=" CA LYS I 11 " pdb=" CB LYS I 11 " ideal model delta sigma weight residual 110.42 152.79 -42.37 1.99e+00 2.53e-01 4.53e+02 angle pdb=" N ARG W 23 " pdb=" CA ARG W 23 " pdb=" C ARG W 23 " ideal model delta sigma weight residual 110.20 79.83 30.37 1.58e+00 4.01e-01 3.70e+02 angle pdb=" N ILE C 14 " pdb=" CA ILE C 14 " pdb=" C ILE C 14 " ideal model delta sigma weight residual 110.53 124.78 -14.25 9.40e-01 1.13e+00 2.30e+02 angle pdb=" O3' G A 266 " pdb=" C3' G A 266 " pdb=" C2' G A 266 " ideal model delta sigma weight residual 109.50 130.75 -21.25 1.50e+00 4.44e-01 2.01e+02 ... (remaining 86195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 29290 35.89 - 71.77: 2171 71.77 - 107.66: 161 107.66 - 143.54: 22 143.54 - 179.43: 45 Dihedral angle restraints: 31689 sinusoidal: 24159 harmonic: 7530 Sorted by residual: dihedral pdb=" C ALA E 21 " pdb=" N ALA E 21 " pdb=" CA ALA E 21 " pdb=" CB ALA E 21 " ideal model delta harmonic sigma weight residual -122.60 -170.07 47.47 0 2.50e+00 1.60e-01 3.61e+02 dihedral pdb=" N ALA E 21 " pdb=" C ALA E 21 " pdb=" CA ALA E 21 " pdb=" CB ALA E 21 " ideal model delta harmonic sigma weight residual 122.90 166.66 -43.76 0 2.50e+00 1.60e-01 3.06e+02 dihedral pdb=" C LYS I 11 " pdb=" N LYS I 11 " pdb=" CA LYS I 11 " pdb=" CB LYS I 11 " ideal model delta harmonic sigma weight residual -122.60 -161.51 38.91 0 2.50e+00 1.60e-01 2.42e+02 ... (remaining 31686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.396: 10733 0.396 - 0.791: 58 0.791 - 1.187: 8 1.187 - 1.583: 1 1.583 - 1.978: 1 Chirality restraints: 10801 Sorted by residual: chirality pdb=" CA ALA E 21 " pdb=" N ALA E 21 " pdb=" C ALA E 21 " pdb=" CB ALA E 21 " both_signs ideal model delta sigma weight residual False 2.48 0.51 1.98 2.00e-01 2.50e+01 9.78e+01 chirality pdb=" CA LYS I 11 " pdb=" N LYS I 11 " pdb=" C LYS I 11 " pdb=" CB LYS I 11 " both_signs ideal model delta sigma weight residual False 2.51 1.03 1.48 2.00e-01 2.50e+01 5.45e+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 -1.63 -1.11 2.00e-01 2.50e+01 3.10e+01 ... (remaining 10798 not shown) Planarity restraints: 5244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 218 " 0.021 2.00e-02 2.50e+03 4.94e-02 5.48e+01 pdb=" N1 C A 218 " -0.015 2.00e-02 2.50e+03 pdb=" C2 C A 218 " 0.003 2.00e-02 2.50e+03 pdb=" O2 C A 218 " 0.051 2.00e-02 2.50e+03 pdb=" N3 C A 218 " -0.119 2.00e-02 2.50e+03 pdb=" C4 C A 218 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C A 218 " 0.066 2.00e-02 2.50e+03 pdb=" C5 C A 218 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C A 218 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A1445 " 0.007 2.00e-02 2.50e+03 4.89e-02 5.38e+01 pdb=" N1 C A1445 " -0.003 2.00e-02 2.50e+03 pdb=" C2 C A1445 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C A1445 " 0.058 2.00e-02 2.50e+03 pdb=" N3 C A1445 " -0.120 2.00e-02 2.50e+03 pdb=" C4 C A1445 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C A1445 " 0.061 2.00e-02 2.50e+03 pdb=" C5 C A1445 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C A1445 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 71 " -0.037 2.00e-02 2.50e+03 4.65e-02 4.86e+01 pdb=" N1 C A 71 " -0.001 2.00e-02 2.50e+03 pdb=" C2 C A 71 " 0.074 2.00e-02 2.50e+03 pdb=" O2 C A 71 " -0.040 2.00e-02 2.50e+03 pdb=" N3 C A 71 " 0.008 2.00e-02 2.50e+03 pdb=" C4 C A 71 " 0.070 2.00e-02 2.50e+03 pdb=" N4 C A 71 " -0.078 2.00e-02 2.50e+03 pdb=" C5 C A 71 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C A 71 " 0.000 2.00e-02 2.50e+03 ... (remaining 5241 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.67: 32 1.67 - 2.48: 172 2.48 - 3.29: 56064 3.29 - 4.09: 178290 4.09 - 4.90: 257714 Warning: very small nonbonded interaction distances. Nonbonded interactions: 492272 Sorted by model distance: nonbonded pdb=" O5' C A 972 " pdb=" CE LYS J 57 " model vdw 0.865 3.440 nonbonded pdb=" O5' C A 972 " pdb=" NZ LYS J 57 " model vdw 0.955 2.520 nonbonded pdb=" OP2 A A 195 " pdb="MG MG A1613 " model vdw 1.013 2.170 nonbonded pdb=" P C A 972 " pdb=" NZ LYS J 57 " model vdw 1.104 3.480 nonbonded pdb=" OP2 A A1499 " pdb="MG MG A1692 " model vdw 1.302 2.170 ... (remaining 492267 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=0.63 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.040 Extract box with map and model: 5.710 Check model and map are aligned: 0.580 Set scattering table: 0.360 Process input model: 152.790 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.130 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: 163.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 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 : 0.009 1.046 58253 Z= 0.522 Angle : 1.470 48.153 86200 Z= 0.977 Chirality : 0.122 1.978 10801 Planarity : 0.009 0.160 5244 Dihedral : 20.860 179.429 26847 Min Nonbonded Distance : 0.865 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 3.61 % Allowed : 10.57 % Favored : 85.82 % Rotamer: Outliers : 20.40 % Allowed : 18.53 % Favored : 61.07 % Cbeta Deviations : 2.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.14), residues: 2574 helix: 0.30 (0.14), residues: 958 sheet: -2.02 (0.24), residues: 386 loop : -3.69 (0.14), residues: 1230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1287 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 448 poor density : 839 time to evaluate : 3.515 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 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 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 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: 448 outliers final: 92 residues processed: 1116 average time/residue: 0.6971 time to fit residues: 1203.9974 Evaluate side-chains 587 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 495 time to evaluate : 2.605 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 0 residues processed: 92 average time/residue: 0.7007 time to fit residues: 102.2054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 340 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 169 optimal weight: 30.0000 chunk 104 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 315 optimal weight: 40.0000 chunk 122 optimal weight: 20.0000 chunk 192 optimal weight: 7.9990 chunk 235 optimal weight: 6.9990 chunk 365 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 113 HIS B 140 HIS B 212 GLN C 28 GLN C 98 ASN C 108 ASN C 123 GLN C 136 GLN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN G 37 ASN G 51 GLN G 96 GLN G 122 HIS ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 GLN K 22 HIS ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN L 9 GLN L 75 HIS M 77 ASN P 65 GLN Q 94 ASN R 36 ASN S 47 HIS T 18 GLN T 75 ASN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 58253 Z= 0.322 Angle : 0.881 14.261 86200 Z= 0.444 Chirality : 0.046 0.327 10801 Planarity : 0.008 0.116 5244 Dihedral : 17.433 175.836 21366 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 31.73 Ramachandran Plot: Outliers : 0.97 % Allowed : 8.90 % Favored : 90.13 % Rotamer: Outliers : 0.46 % Allowed : 7.92 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.16), residues: 2574 helix: 0.78 (0.16), residues: 998 sheet: -1.74 (0.23), residues: 430 loop : -3.04 (0.16), residues: 1146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 657 time to evaluate : 2.606 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 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 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: 10 outliers final: 1 residues processed: 666 average time/residue: 0.6103 time to fit residues: 651.1529 Evaluate side-chains 440 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 439 time to evaluate : 2.832 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3808 time to fit residues: 3.6820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 203 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 chunk 249 optimal weight: 8.9990 chunk 100 optimal weight: 40.0000 chunk 366 optimal weight: 0.0770 chunk 396 optimal weight: 5.9990 chunk 326 optimal weight: 6.9990 chunk 363 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 294 optimal weight: 10.0000 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 108 ASN C 110 ASN D 77 ASN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 ASN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 58253 Z= 0.261 Angle : 0.730 11.780 86200 Z= 0.374 Chirality : 0.040 0.311 10801 Planarity : 0.007 0.121 5244 Dihedral : 16.883 178.538 21366 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 27.08 Ramachandran Plot: Outliers : 0.89 % Allowed : 9.29 % Favored : 89.82 % Rotamer: Outliers : 0.36 % Allowed : 5.42 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -1.70 (0.16), residues: 2574 helix: 0.60 (0.16), residues: 1004 sheet: -1.49 (0.25), residues: 388 loop : -2.61 (0.17), residues: 1182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 584 time to evaluate : 2.696 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 588 average time/residue: 0.6070 time to fit residues: 570.9952 Evaluate side-chains 409 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 407 time to evaluate : 2.612 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4111 time to fit residues: 4.4712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 362 optimal weight: 30.0000 chunk 275 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 246 optimal weight: 30.0000 chunk 367 optimal weight: 30.0000 chunk 389 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 348 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 94 ASN B 140 HIS ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN C 108 ASN C 110 ASN C 123 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 HIS ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 HIS K 26 ASN ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN M 77 ASN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 69 HIS T 42 GLN T 75 ASN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 HIS ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 58253 Z= 0.340 Angle : 0.791 14.194 86200 Z= 0.401 Chirality : 0.042 0.332 10801 Planarity : 0.007 0.125 5244 Dihedral : 17.138 177.840 21366 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 36.31 Ramachandran Plot: Outliers : 0.74 % Allowed : 9.17 % Favored : 90.09 % Rotamer: Outliers : 0.27 % Allowed : 5.15 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.16), residues: 2574 helix: 0.18 (0.16), residues: 1007 sheet: -1.58 (0.25), residues: 410 loop : -2.52 (0.17), residues: 1157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 537 time to evaluate : 2.583 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 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: 6 outliers final: 2 residues processed: 539 average time/residue: 0.6052 time to fit residues: 526.2657 Evaluate side-chains 392 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 390 time to evaluate : 2.579 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4537 time to fit residues: 4.5530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 324 optimal weight: 20.0000 chunk 221 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 290 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 332 optimal weight: 7.9990 chunk 269 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 198 optimal weight: 20.0000 chunk 349 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN M 77 ASN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 GLN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 ASN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 58253 Z= 0.319 Angle : 0.749 12.306 86200 Z= 0.382 Chirality : 0.041 0.332 10801 Planarity : 0.006 0.118 5244 Dihedral : 17.128 179.409 21366 Min Nonbonded Distance : 1.366 Molprobity Statistics. All-atom Clashscore : 34.41 Ramachandran Plot: Outliers : 0.78 % Allowed : 9.09 % Favored : 90.13 % Rotamer: Outliers : 0.14 % Allowed : 4.28 % Favored : 95.58 % 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: -1.90 (0.16), residues: 2574 helix: 0.11 (0.16), residues: 991 sheet: -1.57 (0.25), residues: 422 loop : -2.38 (0.17), residues: 1161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 518 time to evaluate : 2.559 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 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: 3 outliers final: 1 residues processed: 519 average time/residue: 0.5982 time to fit residues: 501.9887 Evaluate side-chains 382 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 381 time to evaluate : 2.580 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4726 time to fit residues: 3.7611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 131 optimal weight: 20.0000 chunk 350 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 228 optimal weight: 9.9990 chunk 96 optimal weight: 30.0000 chunk 389 optimal weight: 8.9990 chunk 323 optimal weight: 20.0000 chunk 180 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 128 optimal weight: 30.0000 chunk 204 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN C 104 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 HIS ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN M 77 ASN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 ASN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 58253 Z= 0.372 Angle : 0.816 23.738 86200 Z= 0.411 Chirality : 0.043 0.373 10801 Planarity : 0.007 0.191 5244 Dihedral : 17.477 179.609 21366 Min Nonbonded Distance : 0.750 Molprobity Statistics. All-atom Clashscore : 41.43 Ramachandran Plot: Outliers : 0.74 % Allowed : 9.83 % Favored : 89.43 % Rotamer: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.63 % 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: -2.25 (0.16), residues: 2574 helix: -0.36 (0.15), residues: 1009 sheet: -1.68 (0.24), residues: 417 loop : -2.46 (0.18), residues: 1148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 481 time to evaluate : 2.600 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 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: 1 outliers final: 0 residues processed: 482 average time/residue: 0.5814 time to fit residues: 457.1528 Evaluate side-chains 360 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 2.608 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 375 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 222 optimal weight: 8.9990 chunk 284 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 328 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 388 optimal weight: 8.9990 chunk 243 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS B 140 HIS C 102 ASN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN C 118 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 HIS ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN M 77 ASN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 26 ASN T 75 ASN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 HIS ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 58253 Z= 0.249 Angle : 0.710 20.715 86200 Z= 0.361 Chirality : 0.039 0.322 10801 Planarity : 0.006 0.180 5244 Dihedral : 17.071 178.218 21366 Min Nonbonded Distance : 1.027 Molprobity Statistics. All-atom Clashscore : 31.67 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.82 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: -1.98 (0.16), residues: 2574 helix: -0.06 (0.16), residues: 996 sheet: -1.58 (0.25), residues: 409 loop : -2.35 (0.18), residues: 1169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 2.603 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 0.5836 time to fit residues: 483.8626 Evaluate side-chains 382 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 2.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 240 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 246 optimal weight: 30.0000 chunk 264 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 305 optimal weight: 9.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN C 102 ASN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN M 77 ASN P 65 GLN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 ASN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.7458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 58253 Z= 0.325 Angle : 0.759 11.945 86200 Z= 0.385 Chirality : 0.041 0.350 10801 Planarity : 0.006 0.105 5244 Dihedral : 17.233 178.885 21366 Min Nonbonded Distance : 0.979 Molprobity Statistics. All-atom Clashscore : 38.86 Ramachandran Plot: Outliers : 0.66 % Allowed : 9.79 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: -2.11 (0.16), residues: 2574 helix: -0.19 (0.16), residues: 989 sheet: -1.67 (0.24), residues: 423 loop : -2.36 (0.18), residues: 1162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 472 time to evaluate : 2.620 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 472 average time/residue: 0.5818 time to fit residues: 453.7853 Evaluate side-chains 342 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 2.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 353 optimal weight: 30.0000 chunk 372 optimal weight: 4.9990 chunk 339 optimal weight: 10.0000 chunk 361 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 284 optimal weight: 0.9990 chunk 111 optimal weight: 30.0000 chunk 327 optimal weight: 8.9990 chunk 342 optimal weight: 10.0000 chunk 360 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN C 102 ASN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN F 57 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 HIS ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN M 77 ASN T 75 ASN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 HIS ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.7538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 58253 Z= 0.217 Angle : 0.680 12.376 86200 Z= 0.347 Chirality : 0.037 0.304 10801 Planarity : 0.006 0.096 5244 Dihedral : 16.814 179.409 21366 Min Nonbonded Distance : 1.035 Molprobity Statistics. All-atom Clashscore : 29.85 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.74 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -1.93 (0.16), residues: 2574 helix: -0.04 (0.16), residues: 979 sheet: -1.71 (0.24), residues: 418 loop : -2.20 (0.18), residues: 1177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 2.614 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.5792 time to fit residues: 478.1773 Evaluate side-chains 365 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 2.598 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 237 optimal weight: 6.9990 chunk 382 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 266 optimal weight: 9.9990 chunk 401 optimal weight: 5.9990 chunk 369 optimal weight: 2.9990 chunk 319 optimal weight: 0.0060 chunk 33 optimal weight: 20.0000 chunk 246 optimal weight: 50.0000 chunk 196 optimal weight: 0.0000 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN C 102 ASN C 108 ASN C 110 ASN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN F 57 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 HIS ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 ASN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 58253 Z= 0.174 Angle : 0.653 14.642 86200 Z= 0.331 Chirality : 0.036 0.284 10801 Planarity : 0.006 0.233 5244 Dihedral : 16.352 179.953 21366 Min Nonbonded Distance : 1.148 Molprobity Statistics. All-atom Clashscore : 25.89 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.00 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.81 (0.16), residues: 2574 helix: 0.02 (0.16), residues: 999 sheet: -1.51 (0.24), residues: 425 loop : -2.18 (0.18), residues: 1150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 2.739 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.5803 time to fit residues: 503.2216 Evaluate side-chains 378 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 2.589 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 253 optimal weight: 5.9990 chunk 340 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 chunk 294 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 320 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 328 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN C 102 ASN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN G 28 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN M 77 ASN M 92 HIS P 65 GLN ** Q 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 ASN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 HIS ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.046123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.037009 restraints weight = 502507.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.038302 restraints weight = 209900.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.039101 restraints weight = 119489.955| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.7909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 58253 Z= 0.326 Angle : 0.757 14.984 86200 Z= 0.383 Chirality : 0.040 0.443 10801 Planarity : 0.007 0.124 5244 Dihedral : 16.816 178.286 21366 Min Nonbonded Distance : 0.957 Molprobity Statistics. All-atom Clashscore : 39.05 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.56 % Favored : 89.94 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -1.93 (0.16), residues: 2574 helix: -0.14 (0.16), residues: 971 sheet: -1.52 (0.24), residues: 419 loop : -2.17 (0.18), residues: 1184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9781.76 seconds wall clock time: 175 minutes 36.08 seconds (10536.08 seconds total)