Starting phenix.real_space_refine (version: dev) on Mon Dec 12 22:13:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/12_2022/7cgp_9958_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/12_2022/7cgp_9958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/12_2022/7cgp_9958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/12_2022/7cgp_9958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/12_2022/7cgp_9958_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/12_2022/7cgp_9958_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 37": "NH1" <-> "NH2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "F GLU 50": "OE1" <-> "OE2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "H ARG 31": "NH1" <-> "NH2" Residue "H GLU 40": "OE1" <-> "OE2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I GLU 40": "OE1" <-> "OE2" Residue "I GLU 63": "OE1" <-> "OE2" Residue "J ARG 23": "NH1" <-> "NH2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K ARG 39": "NH1" <-> "NH2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "M GLU 12": "OE1" <-> "OE2" Residue "M GLU 14": "OE1" <-> "OE2" Residue "M ARG 24": "NH1" <-> "NH2" Residue "N GLU 14": "OE1" <-> "OE2" Residue "N GLU 40": "OE1" <-> "OE2" Residue "N GLU 71": "OE1" <-> "OE2" Residue "O ARG 5": "NH1" <-> "NH2" Residue "O ARG 24": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 12433 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1068 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain breaks: 1 Chain: "B" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2696 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 326} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1684 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 10, 'TRANS': 212} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5, 'TRP:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "D" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 554 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 64} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 558 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 64} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 521 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 61} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 569 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 551 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 502 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 61} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "J" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 680 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "K" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 590 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "L" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 646 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "M" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 589 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 580 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "O" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.72, per 1000 atoms: 0.62 Number of scatterers: 12433 At special positions: 0 Unit cell: (121.68, 113.568, 172.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 122 16.00 P 1 15.00 O 2329 8.00 N 2158 7.00 C 7823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 141 " distance=2.02 Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 52 " distance=2.04 Simple disulfide: pdb=" SG CYS D 32 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 52 " distance=2.03 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS E 48 " distance=2.03 Simple disulfide: pdb=" SG CYS F 28 " - pdb=" SG CYS F 52 " distance=2.03 Simple disulfide: pdb=" SG CYS F 32 " - pdb=" SG CYS F 48 " distance=2.03 Simple disulfide: pdb=" SG CYS G 29 " - pdb=" SG CYS G 54 " distance=2.03 Simple disulfide: pdb=" SG CYS G 33 " - pdb=" SG CYS G 50 " distance=2.03 Simple disulfide: pdb=" SG CYS H 29 " - pdb=" SG CYS H 54 " distance=2.03 Simple disulfide: pdb=" SG CYS H 33 " - pdb=" SG CYS H 50 " distance=2.03 Simple disulfide: pdb=" SG CYS I 29 " - pdb=" SG CYS I 54 " distance=2.03 Simple disulfide: pdb=" SG CYS I 33 " - pdb=" SG CYS I 50 " distance=2.02 Simple disulfide: pdb=" SG CYS J 28 " - pdb=" SG CYS J 52 " distance=2.03 Simple disulfide: pdb=" SG CYS J 32 " - pdb=" SG CYS J 48 " distance=2.03 Simple disulfide: pdb=" SG CYS K 28 " - pdb=" SG CYS K 52 " distance=2.03 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 48 " distance=2.03 Simple disulfide: pdb=" SG CYS L 28 " - pdb=" SG CYS L 52 " distance=2.04 Simple disulfide: pdb=" SG CYS L 32 " - pdb=" SG CYS L 48 " distance=2.03 Simple disulfide: pdb=" SG CYS M 29 " - pdb=" SG CYS M 54 " distance=2.04 Simple disulfide: pdb=" SG CYS M 33 " - pdb=" SG CYS M 50 " distance=2.03 Simple disulfide: pdb=" SG CYS N 29 " - pdb=" SG CYS N 54 " distance=2.03 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 50 " distance=2.02 Simple disulfide: pdb=" SG CYS O 29 " - pdb=" SG CYS O 54 " distance=2.04 Simple disulfide: pdb=" SG CYS O 33 " - pdb=" SG CYS O 50 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.65 Conformation dependent library (CDL) restraints added in 1.9 seconds 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 4 sheets defined 66.5% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 25 through 32 removed outlier: 4.342A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 69 through 92 Processing helix chain 'A' and resid 121 through 147 Processing helix chain 'A' and resid 152 through 170 Processing helix chain 'A' and resid 172 through 192 removed outlier: 3.572A pdb=" N ALA A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLY A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 50 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 103 through 111 Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.609A pdb=" N LEU B 164 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 184 removed outlier: 3.956A pdb=" N ILE B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.940A pdb=" N ILE B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS B 233 " --> pdb=" O PRO B 229 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N HIS B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.720A pdb=" N ARG B 351 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'C' and resid 22 through 54 Processing helix chain 'C' and resid 58 through 74 Processing helix chain 'C' and resid 79 through 96 removed outlier: 4.557A pdb=" N GLU C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 118 Processing helix chain 'C' and resid 145 through 148 No H-bonds generated for 'chain 'C' and resid 145 through 148' Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 175 through 178 No H-bonds generated for 'chain 'C' and resid 175 through 178' Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.092A pdb=" N LYS C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 243 Processing helix chain 'D' and resid 14 through 31 Processing helix chain 'D' and resid 43 through 76 removed outlier: 3.631A pdb=" N LEU D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 29 removed outlier: 4.037A pdb=" N GLU E 26 " --> pdb=" O ASN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 74 Processing helix chain 'F' and resid 15 through 32 Processing helix chain 'F' and resid 43 through 74 removed outlier: 4.130A pdb=" N GLN F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 32 removed outlier: 3.621A pdb=" N MET G 21 " --> pdb=" O MET G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.114A pdb=" N ASP G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU G 72 " --> pdb=" O LYS G 68 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET G 74 " --> pdb=" O THR G 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 33 Processing helix chain 'H' and resid 45 through 74 removed outlier: 4.004A pdb=" N ASP H 52 " --> pdb=" O SER H 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 33 removed outlier: 3.746A pdb=" N SER I 27 " --> pdb=" O ASN I 23 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG I 31 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS I 32 " --> pdb=" O ALA I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 48 No H-bonds generated for 'chain 'I' and resid 45 through 48' Processing helix chain 'I' and resid 50 through 72 removed outlier: 4.013A pdb=" N SER I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS I 68 " --> pdb=" O ARG I 64 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU I 72 " --> pdb=" O LYS I 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 30 Processing helix chain 'J' and resid 43 through 84 Proline residue: J 72 - end of helix Processing helix chain 'K' and resid 9 through 32 Processing helix chain 'K' and resid 46 through 76 removed outlier: 3.998A pdb=" N GLU K 50 " --> pdb=" O THR K 46 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 32 removed outlier: 3.784A pdb=" N GLN L 10 " --> pdb=" O PRO L 6 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN L 13 " --> pdb=" O ASP L 9 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR L 27 " --> pdb=" O LYS L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 81 removed outlier: 4.397A pdb=" N SER L 49 " --> pdb=" O GLU L 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 33 Processing helix chain 'M' and resid 46 through 74 removed outlier: 4.673A pdb=" N LEU M 51 " --> pdb=" O GLU M 47 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE M 61 " --> pdb=" O LYS M 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 33 removed outlier: 3.593A pdb=" N CYS N 33 " --> pdb=" O CYS N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 58 removed outlier: 3.881A pdb=" N ASP N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER N 56 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 72 removed outlier: 3.752A pdb=" N GLY N 66 " --> pdb=" O HIS N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 33 removed outlier: 3.970A pdb=" N SER O 27 " --> pdb=" O ASN O 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG O 31 " --> pdb=" O SER O 27 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 76 removed outlier: 4.116A pdb=" N ASP O 52 " --> pdb=" O SER O 48 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS O 57 " --> pdb=" O ARG O 53 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU O 59 " --> pdb=" O VAL O 55 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP O 60 " --> pdb=" O SER O 56 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 94 through 99 removed outlier: 7.041A pdb=" N VAL B 118 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N PHE B 66 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 120 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N VAL B 121 " --> pdb=" O PRO B 148 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY B 150 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 188 through 190 Processing sheet with id= C, first strand: chain 'B' and resid 202 through 205 Processing sheet with id= D, first strand: chain 'B' and resid 208 through 212 804 hydrogen bonds defined for protein. 2391 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2477 1.33 - 1.45: 2878 1.45 - 1.58: 7115 1.58 - 1.70: 2 1.70 - 1.82: 179 Bond restraints: 12651 Sorted by residual: bond pdb=" N VAL C 22 " pdb=" CA VAL C 22 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.98e+00 bond pdb=" N VAL C 27 " pdb=" CA VAL C 27 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.70e+00 bond pdb=" N LEU B 227 " pdb=" CA LEU B 227 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.19e-02 7.06e+03 7.53e+00 bond pdb=" N LYS C 24 " pdb=" CA LYS C 24 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.04e-02 9.25e+03 7.43e+00 bond pdb=" N THR B 157 " pdb=" CA THR B 157 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.27e-02 6.20e+03 7.08e+00 ... (remaining 12646 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.91: 247 105.91 - 113.00: 6851 113.00 - 120.09: 4600 120.09 - 127.18: 5196 127.18 - 134.27: 114 Bond angle restraints: 17008 Sorted by residual: angle pdb=" N VAL M 49 " pdb=" CA VAL M 49 " pdb=" C VAL M 49 " ideal model delta sigma weight residual 112.96 108.20 4.76 1.00e+00 1.00e+00 2.27e+01 angle pdb=" N LEU B 154 " pdb=" CA LEU B 154 " pdb=" C LEU B 154 " ideal model delta sigma weight residual 112.89 108.17 4.72 1.24e+00 6.50e-01 1.45e+01 angle pdb=" C ASP F 31 " pdb=" N CYS F 32 " pdb=" CA CYS F 32 " ideal model delta sigma weight residual 122.56 117.21 5.35 1.50e+00 4.44e-01 1.27e+01 angle pdb=" N ARG C 197 " pdb=" CA ARG C 197 " pdb=" C ARG C 197 " ideal model delta sigma weight residual 113.50 109.23 4.27 1.23e+00 6.61e-01 1.21e+01 angle pdb=" O3P PEE C 301 " pdb=" P PEE C 301 " pdb=" O4P PEE C 301 " ideal model delta sigma weight residual 92.91 103.08 -10.17 3.00e+00 1.11e-01 1.15e+01 ... (remaining 17003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.31: 7365 24.31 - 48.63: 423 48.63 - 72.94: 42 72.94 - 97.26: 13 97.26 - 121.57: 1 Dihedral angle restraints: 7844 sinusoidal: 3264 harmonic: 4580 Sorted by residual: dihedral pdb=" CB CYS F 32 " pdb=" SG CYS F 32 " pdb=" SG CYS F 48 " pdb=" CB CYS F 48 " ideal model delta sinusoidal sigma weight residual 93.00 52.07 40.93 1 1.00e+01 1.00e-02 2.35e+01 dihedral pdb=" CA CYS N 33 " pdb=" C CYS N 33 " pdb=" N VAL N 34 " pdb=" CA VAL N 34 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CB CYS D 32 " pdb=" SG CYS D 32 " pdb=" SG CYS D 48 " pdb=" CB CYS D 48 " ideal model delta sinusoidal sigma weight residual 93.00 56.44 36.56 1 1.00e+01 1.00e-02 1.89e+01 ... (remaining 7841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1558 0.051 - 0.102: 262 0.102 - 0.153: 43 0.153 - 0.204: 9 0.204 - 0.254: 1 Chirality restraints: 1873 Sorted by residual: chirality pdb=" CA VAL C 198 " pdb=" N VAL C 198 " pdb=" C VAL C 198 " pdb=" CB VAL C 198 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA LEU B 154 " pdb=" N LEU B 154 " pdb=" C LEU B 154 " pdb=" CB LEU B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA VAL C 27 " pdb=" N VAL C 27 " pdb=" C VAL C 27 " pdb=" CB VAL C 27 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 1870 not shown) Planarity restraints: 2183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 196 " 0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C LEU C 196 " -0.071 2.00e-02 2.50e+03 pdb=" O LEU C 196 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG C 197 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 34 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO G 35 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO G 35 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 35 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU N 47 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C GLU N 47 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU N 47 " -0.010 2.00e-02 2.50e+03 pdb=" N SER N 48 " -0.009 2.00e-02 2.50e+03 ... (remaining 2180 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 79 2.46 - 3.07: 9319 3.07 - 3.68: 18777 3.68 - 4.29: 25805 4.29 - 4.90: 42724 Nonbonded interactions: 96704 Sorted by model distance: nonbonded pdb=" OH TYR D 70 " pdb=" OE2 GLU G 63 " model vdw 1.852 2.440 nonbonded pdb=" O ILE B 335 " pdb=" OG1 THR B 363 " model vdw 1.882 2.440 nonbonded pdb=" NE2 GLN K 74 " pdb=" OE2 GLU O 63 " model vdw 1.951 2.520 nonbonded pdb=" OE2 GLU A 144 " pdb=" OG SER A 150 " model vdw 2.036 2.440 nonbonded pdb=" OH TYR F 21 " pdb=" O HIS G 62 " model vdw 2.068 2.440 ... (remaining 96699 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 13 through 72 or (resid 73 through 75 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 13 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 73 or (resid 74 through 75 and (na \ me N or name CA or name C or name O or name CB )))) selection = chain 'F' selection = (chain 'K' and (resid 13 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 72 or (resid 73 through 75 and (na \ me N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'G' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 67 or (resid 68 and ( \ name N or name CA or name C or name O or name CB )) or resid 69 through 72 or (r \ esid 73 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 67 or (resid 68 and (name N or nam \ e CA or name C or name O or name CB )) or resid 69 through 72 or (resid 73 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'I' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 73)) selection = (chain 'M' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 67 or (resid 68 and ( \ name N or name CA or name C or name O or name CB )) or resid 69 through 72 or (r \ esid 73 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'N' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 67 or (resid 68 and ( \ name N or name CA or name C or name O or name CB )) or resid 69 through 72 or (r \ esid 73 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'O' and (resid 10 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 67 or (resid 68 and (name N or nam \ e CA or name C or name O or name CB )) or resid 69 through 72 or (resid 73 and ( \ name N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 122 5.16 5 C 7823 2.51 5 N 2158 2.21 5 O 2329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.180 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: 0.010 Extract box with map and model: 7.960 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.100 Process input model: 35.650 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.006 0.057 12651 Z= 0.400 Angle : 0.659 10.173 17008 Z= 0.424 Chirality : 0.041 0.254 1873 Planarity : 0.003 0.050 2183 Dihedral : 14.706 121.569 4790 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 0.53 % 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: -2.68 (0.19), residues: 1531 helix: -0.96 (0.14), residues: 1038 sheet: -2.91 (0.44), residues: 105 loop : -3.36 (0.26), residues: 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 582 time to evaluate : 1.519 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 outliers start: 7 outliers final: 5 residues processed: 586 average time/residue: 0.2918 time to fit residues: 228.1635 Evaluate side-chains 420 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 415 time to evaluate : 1.554 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1126 time to fit residues: 3.1482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 71 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 HIS C 203 GLN E 54 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 HIS I 37 HIS I 62 HIS ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 71 HIS L 71 HIS L 74 GLN M 30 HIS N 8 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 12651 Z= 0.244 Angle : 0.744 12.404 17008 Z= 0.376 Chirality : 0.044 0.289 1873 Planarity : 0.005 0.045 2183 Dihedral : 7.341 92.895 1726 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 3.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1531 helix: 0.95 (0.16), residues: 1033 sheet: -2.32 (0.40), residues: 114 loop : -2.23 (0.31), residues: 384 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 482 time to evaluate : 1.576 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 outliers start: 48 outliers final: 28 residues processed: 494 average time/residue: 0.3131 time to fit residues: 210.9916 Evaluate side-chains 437 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 409 time to evaluate : 1.605 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 28 outliers final: 1 residues processed: 28 average time/residue: 0.1398 time to fit residues: 8.9169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 110 optimal weight: 0.1980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 HIS F 61 GLN I 37 HIS ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN K 22 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 12651 Z= 0.238 Angle : 0.701 10.494 17008 Z= 0.359 Chirality : 0.043 0.214 1873 Planarity : 0.004 0.043 2183 Dihedral : 6.938 78.735 1726 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.22), residues: 1531 helix: 1.30 (0.16), residues: 1041 sheet: -1.74 (0.43), residues: 115 loop : -1.90 (0.32), residues: 375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 461 time to evaluate : 1.549 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 outliers start: 51 outliers final: 23 residues processed: 486 average time/residue: 0.2759 time to fit residues: 184.6361 Evaluate side-chains 433 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 410 time to evaluate : 1.620 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1328 time to fit residues: 7.7371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS K 13 GLN K 71 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 12651 Z= 0.324 Angle : 0.737 11.464 17008 Z= 0.375 Chirality : 0.046 0.319 1873 Planarity : 0.004 0.039 2183 Dihedral : 6.881 76.103 1726 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1531 helix: 1.34 (0.16), residues: 1049 sheet: -1.41 (0.47), residues: 108 loop : -1.94 (0.31), residues: 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 433 time to evaluate : 1.666 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 outliers start: 53 outliers final: 25 residues processed: 460 average time/residue: 0.2768 time to fit residues: 174.9078 Evaluate side-chains 419 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 394 time to evaluate : 1.634 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1159 time to fit residues: 7.5821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 GLN E 51 HIS ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN M 62 HIS ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 12651 Z= 0.248 Angle : 0.729 11.424 17008 Z= 0.368 Chirality : 0.044 0.274 1873 Planarity : 0.004 0.042 2183 Dihedral : 6.678 79.235 1726 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.22), residues: 1531 helix: 1.43 (0.16), residues: 1047 sheet: -1.30 (0.45), residues: 115 loop : -1.73 (0.33), residues: 369 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 426 time to evaluate : 1.713 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 outliers start: 41 outliers final: 14 residues processed: 447 average time/residue: 0.2692 time to fit residues: 165.6395 Evaluate side-chains 414 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 400 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1197 time to fit residues: 5.2233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 146 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS E 74 GLN ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 GLN ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.094 12651 Z= 0.267 Angle : 0.763 11.781 17008 Z= 0.387 Chirality : 0.044 0.251 1873 Planarity : 0.004 0.040 2183 Dihedral : 6.564 78.800 1726 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1531 helix: 1.46 (0.16), residues: 1035 sheet: -1.40 (0.51), residues: 95 loop : -1.66 (0.31), residues: 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 426 time to evaluate : 1.423 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 outliers start: 38 outliers final: 22 residues processed: 442 average time/residue: 0.2775 time to fit residues: 166.9884 Evaluate side-chains 423 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 401 time to evaluate : 1.751 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1365 time to fit residues: 7.2179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS I 37 HIS ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 12651 Z= 0.246 Angle : 0.778 13.405 17008 Z= 0.390 Chirality : 0.044 0.302 1873 Planarity : 0.004 0.054 2183 Dihedral : 6.438 79.865 1726 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1531 helix: 1.42 (0.16), residues: 1034 sheet: -1.34 (0.51), residues: 95 loop : -1.60 (0.31), residues: 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 431 time to evaluate : 1.674 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 outliers start: 24 outliers final: 14 residues processed: 439 average time/residue: 0.2863 time to fit residues: 171.0858 Evaluate side-chains 413 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 399 time to evaluate : 1.602 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1114 time to fit residues: 5.0316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 114 optimal weight: 0.0980 chunk 132 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 12651 Z= 0.270 Angle : 0.815 14.193 17008 Z= 0.413 Chirality : 0.045 0.258 1873 Planarity : 0.004 0.040 2183 Dihedral : 6.321 79.454 1726 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1531 helix: 1.38 (0.16), residues: 1036 sheet: -1.31 (0.52), residues: 95 loop : -1.55 (0.30), residues: 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 417 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 428 average time/residue: 0.2919 time to fit residues: 169.4846 Evaluate side-chains 414 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 398 time to evaluate : 1.603 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1421 time to fit residues: 5.9331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 chunk 135 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 59 optimal weight: 0.0370 chunk 106 optimal weight: 30.0000 chunk 41 optimal weight: 0.0270 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 HIS O 30 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 12651 Z= 0.237 Angle : 0.860 14.979 17008 Z= 0.432 Chirality : 0.045 0.279 1873 Planarity : 0.004 0.043 2183 Dihedral : 6.176 82.319 1726 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1531 helix: 1.36 (0.16), residues: 1031 sheet: -0.84 (0.54), residues: 89 loop : -1.58 (0.30), residues: 411 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 435 time to evaluate : 1.619 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 outliers start: 12 outliers final: 6 residues processed: 441 average time/residue: 0.2946 time to fit residues: 176.3519 Evaluate side-chains 410 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 404 time to evaluate : 1.535 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1195 time to fit residues: 3.5502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 174 HIS B 248 HIS ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS K 13 GLN O 8 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.077 12651 Z= 0.393 Angle : 0.897 14.166 17008 Z= 0.463 Chirality : 0.049 0.270 1873 Planarity : 0.005 0.048 2183 Dihedral : 6.134 72.880 1726 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.22), residues: 1531 helix: 1.21 (0.16), residues: 1042 sheet: -1.32 (0.53), residues: 93 loop : -1.55 (0.31), residues: 396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 410 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 415 average time/residue: 0.2779 time to fit residues: 157.4973 Evaluate side-chains 400 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 389 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1212 time to fit residues: 4.4914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 50 optimal weight: 50.0000 chunk 123 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 HIS C 141 GLN D 54 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN M 7 GLN O 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.116895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.091862 restraints weight = 29571.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.090975 restraints weight = 21825.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.092025 restraints weight = 21010.386| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 12651 Z= 0.319 Angle : 0.918 14.259 17008 Z= 0.470 Chirality : 0.048 0.315 1873 Planarity : 0.004 0.038 2183 Dihedral : 5.978 73.521 1726 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.22), residues: 1531 helix: 1.14 (0.16), residues: 1046 sheet: -1.28 (0.53), residues: 93 loop : -1.49 (0.31), residues: 392 =============================================================================== Job complete usr+sys time: 3321.10 seconds wall clock time: 60 minutes 54.99 seconds (3654.99 seconds total)