Starting phenix.real_space_refine (version: dev) on Wed Feb 22 23:03:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifu_9657/02_2023/6ifu_9657.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifu_9657/02_2023/6ifu_9657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifu_9657/02_2023/6ifu_9657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifu_9657/02_2023/6ifu_9657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifu_9657/02_2023/6ifu_9657.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifu_9657/02_2023/6ifu_9657.pdb" } resolution = 3.05 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= 0.026 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 Process input model Symmetric amino acids flipped Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "B TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 6": "NH1" <-> "NH2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "H TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18750 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5561 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 8, 'TRANS': 697} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 975 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 975 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1690 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 209} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1626 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2163 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "H" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2744 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 715 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 17} Chain: "J" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 606 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 24} Time building chain proxies: 10.73, per 1000 atoms: 0.57 Number of scatterers: 18750 At special positions: 0 Unit cell: (92.56, 135.2, 170.56, 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 39 16.00 P 62 15.00 O 3707 8.00 N 3178 7.00 C 11764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.01 Conformation dependent library (CDL) restraints added in 2.8 seconds 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 21 sheets defined 38.9% alpha, 11.0% beta 22 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 5.22 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.504A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.553A pdb=" N SER A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 3.797A pdb=" N GLY A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.786A pdb=" N ALA A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 180 removed outlier: 3.728A pdb=" N LEU A 173 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 265 through 291 Processing helix chain 'A' and resid 315 through 335 Processing helix chain 'A' and resid 349 through 354 removed outlier: 3.850A pdb=" N ILE A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 354' Processing helix chain 'A' and resid 359 through 380 removed outlier: 3.901A pdb=" N TYR A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 392 removed outlier: 3.857A pdb=" N MET A 388 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 432 removed outlier: 4.126A pdb=" N LYS A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.701A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 556 removed outlier: 3.630A pdb=" N PHE A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 563 removed outlier: 3.850A pdb=" N GLN A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.511A pdb=" N ALA A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 629 through 637 Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.527A pdb=" N ILE A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 712 removed outlier: 3.637A pdb=" N GLU A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 738 through 755 removed outlier: 4.166A pdb=" N LYS A 742 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 Processing helix chain 'B' and resid 36 through 57 removed outlier: 3.830A pdb=" N LEU B 46 " --> pdb=" O ASN B 42 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 80 removed outlier: 3.637A pdb=" N LEU B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ARG B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.568A pdb=" N LYS B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 97 removed outlier: 3.798A pdb=" N LYS B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 122 removed outlier: 3.649A pdb=" N LEU B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.645A pdb=" N ALA C 13 " --> pdb=" O TYR C 9 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 55 removed outlier: 3.622A pdb=" N LEU C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 55 " --> pdb=" O PHE C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 62 through 80 removed outlier: 3.924A pdb=" N ARG C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 77 " --> pdb=" O PHE C 73 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.529A pdb=" N LYS C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 122 removed outlier: 3.616A pdb=" N ARG C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 113 " --> pdb=" O CYS C 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.710A pdb=" N SER D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 178 removed outlier: 3.535A pdb=" N VAL D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 71 through 75 Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.919A pdb=" N LEU E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.971A pdb=" N LYS E 92 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 159 through 162 Processing helix chain 'E' and resid 163 through 178 removed outlier: 4.129A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.829A pdb=" N GLY E 189 " --> pdb=" O GLY E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.673A pdb=" N THR E 211 " --> pdb=" O ASP E 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 60 removed outlier: 3.582A pdb=" N LYS F 55 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU F 60 " --> pdb=" O MET F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 84 removed outlier: 3.507A pdb=" N LEU F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 113 Processing helix chain 'F' and resid 156 through 162 removed outlier: 4.126A pdb=" N GLN F 162 " --> pdb=" O GLU F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 165 No H-bonds generated for 'chain 'F' and resid 163 through 165' Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.660A pdb=" N ILE F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG F 171 " --> pdb=" O PHE F 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 166 through 171' Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'G' and resid 29 through 42 removed outlier: 4.042A pdb=" N LYS G 42 " --> pdb=" O LEU G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 54 Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 163 through 177 removed outlier: 3.804A pdb=" N SER G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 230 removed outlier: 4.342A pdb=" N GLU G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 52 removed outlier: 3.646A pdb=" N GLU H 52 " --> pdb=" O ASN H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.811A pdb=" N ILE H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 74 removed outlier: 4.240A pdb=" N ARG H 74 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 82 removed outlier: 3.602A pdb=" N LEU H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN H 82 " --> pdb=" O PHE H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 143 removed outlier: 3.548A pdb=" N ILE H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 183 Processing helix chain 'H' and resid 236 through 259 removed outlier: 5.325A pdb=" N GLY H 247 " --> pdb=" O ILE H 243 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS H 248 " --> pdb=" O GLU H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 295 Processing helix chain 'H' and resid 296 through 301 Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 438 removed outlier: 3.701A pdb=" N HIS A 436 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 569 through 574 removed outlier: 6.815A pdb=" N PHE A 580 " --> pdb=" O ILE A 572 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 519 through 520 removed outlier: 3.538A pdb=" N ASP A 519 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 644 through 645 removed outlier: 3.616A pdb=" N PHE A 653 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 96 through 98 removed outlier: 6.303A pdb=" N LYS D 5 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN D 11 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASN D 197 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG D 13 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE D 195 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 122 Processing sheet with id=AA9, first strand: chain 'E' and resid 96 through 98 removed outlier: 6.394A pdb=" N LYS E 5 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLN E 11 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASN E 197 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG E 13 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE E 195 " --> pdb=" O ARG E 13 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 126 Processing sheet with id=AB2, first strand: chain 'F' and resid 96 through 97 removed outlier: 3.585A pdb=" N LEU F 151 " --> pdb=" O PHE F 8 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS F 5 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR F 202 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS F 7 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA F 200 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER F 9 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU F 198 " --> pdb=" O SER F 9 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 118 through 123 Processing sheet with id=AB4, first strand: chain 'G' and resid 159 through 160 Processing sheet with id=AB5, first strand: chain 'G' and resid 71 through 73 Processing sheet with id=AB6, first strand: chain 'G' and resid 126 through 132 Processing sheet with id=AB7, first strand: chain 'G' and resid 265 through 266 Processing sheet with id=AB8, first strand: chain 'G' and resid 273 through 274 Processing sheet with id=AB9, first strand: chain 'H' and resid 184 through 186 Processing sheet with id=AC1, first strand: chain 'H' and resid 32 through 33 Processing sheet with id=AC2, first strand: chain 'H' and resid 113 through 115 removed outlier: 6.051A pdb=" N GLU H 113 " --> pdb=" O TYR H 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'H' and resid 212 through 214 639 hydrogen bonds defined for protein. 1821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 5.34 Time building geometry restraints manager: 8.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3316 1.32 - 1.44: 5302 1.44 - 1.57: 10417 1.57 - 1.69: 125 1.69 - 1.81: 70 Bond restraints: 19230 Sorted by residual: bond pdb=" CB ARG E 136 " pdb=" CG ARG E 136 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 8.00e+00 bond pdb=" CB VAL A 516 " pdb=" CG2 VAL A 516 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.70e+00 bond pdb=" CG LEU F 18 " pdb=" CD2 LEU F 18 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.18e+00 bond pdb=" CB LEU F 18 " pdb=" CG LEU F 18 " ideal model delta sigma weight residual 1.530 1.477 0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" CB ARG C 65 " pdb=" CG ARG C 65 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 7.02e+00 ... (remaining 19225 not shown) Histogram of bond angle deviations from ideal: 95.79 - 104.22: 431 104.22 - 112.65: 9599 112.65 - 121.08: 10993 121.08 - 129.51: 5099 129.51 - 137.94: 110 Bond angle restraints: 26232 Sorted by residual: angle pdb=" N LYS H 146 " pdb=" CA LYS H 146 " pdb=" C LYS H 146 " ideal model delta sigma weight residual 114.62 105.55 9.07 1.14e+00 7.69e-01 6.33e+01 angle pdb=" N PRO A 143 " pdb=" CA PRO A 143 " pdb=" CB PRO A 143 " ideal model delta sigma weight residual 103.25 111.40 -8.15 1.05e+00 9.07e-01 6.03e+01 angle pdb=" N PHE A 658 " pdb=" CA PHE A 658 " pdb=" C PHE A 658 " ideal model delta sigma weight residual 110.80 95.79 15.01 2.13e+00 2.20e-01 4.96e+01 angle pdb=" C LEU A 646 " pdb=" N PHE A 647 " pdb=" CA PHE A 647 " ideal model delta sigma weight residual 120.82 130.67 -9.85 1.50e+00 4.44e-01 4.32e+01 angle pdb=" CA LEU H 199 " pdb=" CB LEU H 199 " pdb=" CG LEU H 199 " ideal model delta sigma weight residual 116.30 137.94 -21.64 3.50e+00 8.16e-02 3.82e+01 ... (remaining 26227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.39: 11087 29.39 - 58.78: 293 58.78 - 88.16: 15 88.16 - 117.55: 5 117.55 - 146.94: 4 Dihedral angle restraints: 11404 sinusoidal: 4972 harmonic: 6432 Sorted by residual: dihedral pdb=" CA ASP E 157 " pdb=" C ASP E 157 " pdb=" N GLU E 158 " pdb=" CA GLU E 158 " ideal model delta harmonic sigma weight residual 180.00 -122.67 -57.33 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA SER E 185 " pdb=" C SER E 185 " pdb=" N GLY E 186 " pdb=" CA GLY E 186 " ideal model delta harmonic sigma weight residual 180.00 128.80 51.20 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA VAL F 203 " pdb=" C VAL F 203 " pdb=" N PHE F 204 " pdb=" CA PHE F 204 " ideal model delta harmonic sigma weight residual -180.00 -135.05 -44.95 0 5.00e+00 4.00e-02 8.08e+01 ... (remaining 11401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2575 0.106 - 0.211: 353 0.211 - 0.317: 30 0.317 - 0.422: 11 0.422 - 0.528: 3 Chirality restraints: 2972 Sorted by residual: chirality pdb=" CB VAL F 193 " pdb=" CA VAL F 193 " pdb=" CG1 VAL F 193 " pdb=" CG2 VAL F 193 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CB ILE A 644 " pdb=" CA ILE A 644 " pdb=" CG1 ILE A 644 " pdb=" CG2 ILE A 644 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CB ILE F 12 " pdb=" CA ILE F 12 " pdb=" CG1 ILE F 12 " pdb=" CG2 ILE F 12 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 2969 not shown) Planarity restraints: 3141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A I 27 " 0.070 2.00e-02 2.50e+03 3.22e-02 2.86e+01 pdb=" N9 A I 27 " -0.076 2.00e-02 2.50e+03 pdb=" C8 A I 27 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A I 27 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A I 27 " 0.006 2.00e-02 2.50e+03 pdb=" C6 A I 27 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A I 27 " 0.019 2.00e-02 2.50e+03 pdb=" N1 A I 27 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A I 27 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A I 27 " -0.011 2.00e-02 2.50e+03 pdb=" C4 A I 27 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G I 21 " 0.066 2.00e-02 2.50e+03 2.89e-02 2.50e+01 pdb=" N9 G I 21 " -0.069 2.00e-02 2.50e+03 pdb=" C8 G I 21 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G I 21 " -0.007 2.00e-02 2.50e+03 pdb=" C5 G I 21 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G I 21 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G I 21 " 0.024 2.00e-02 2.50e+03 pdb=" N1 G I 21 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G I 21 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G I 21 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G I 21 " -0.010 2.00e-02 2.50e+03 pdb=" C4 G I 21 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 19 " -0.052 2.00e-02 2.50e+03 2.74e-02 1.69e+01 pdb=" N1 U I 19 " 0.059 2.00e-02 2.50e+03 pdb=" C2 U I 19 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U I 19 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U I 19 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U I 19 " -0.012 2.00e-02 2.50e+03 pdb=" O4 U I 19 " -0.015 2.00e-02 2.50e+03 pdb=" C5 U I 19 " 0.004 2.00e-02 2.50e+03 pdb=" C6 U I 19 " 0.008 2.00e-02 2.50e+03 ... (remaining 3138 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2881 2.75 - 3.28: 17610 3.28 - 3.82: 32700 3.82 - 4.36: 40530 4.36 - 4.90: 67785 Nonbonded interactions: 161506 Sorted by model distance: nonbonded pdb=" OG1 THR D 125 " pdb=" O2 U I 25 " model vdw 2.207 2.440 nonbonded pdb=" O PHE G 71 " pdb=" OH TYR G 157 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR D 16 " pdb=" OD2 ASP H 188 " model vdw 2.267 2.440 nonbonded pdb=" OD2 ASP G 62 " pdb=" OG SER G 262 " model vdw 2.282 2.440 nonbonded pdb=" OD2 ASP D 100 " pdb=" NH2 ARG E 140 " model vdw 2.289 2.520 ... (remaining 161501 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 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 66 or resid 76 through 217)) selection = (chain 'E' and (resid 2 through 66 or resid 76 through 217)) selection = (chain 'F' and (resid 2 through 159 or (resid 160 and (name N or name CA or name \ C or name O or name CB )) or resid 161 through 217)) } 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 62 5.49 5 S 39 5.16 5 C 11764 2.51 5 N 3178 2.21 5 O 3707 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 0.020 Extract box with map and model: 3.540 Check model and map are aligned: 0.290 Process input model: 52.290 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.012 0.127 19230 Z= 0.793 Angle : 1.401 21.643 26232 Z= 0.738 Chirality : 0.076 0.528 2972 Planarity : 0.008 0.056 3141 Dihedral : 13.488 146.940 7256 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.69 % Allowed : 13.89 % Favored : 85.42 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.99 % 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: -4.96 (0.14), residues: 2167 helix: -3.23 (0.12), residues: 798 sheet: -2.87 (0.24), residues: 336 loop : -3.47 (0.15), residues: 1033 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 544 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 559 average time/residue: 0.3737 time to fit residues: 298.6562 Evaluate side-chains 333 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 324 time to evaluate : 2.048 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1735 time to fit residues: 5.6990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 257 ASN A 297 ASN A 312 ASN A 391 ASN A 536 ASN A 562 GLN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN A 699 ASN A 735 ASN C 76 GLN D 134 ASN D 159 ASN E 11 GLN E 33 ASN ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 144 ASN E 197 ASN E 213 ASN F 11 GLN F 134 ASN F 159 ASN F 161 ASN F 197 ASN G 14 HIS G 144 GLN G 273 GLN G 284 HIS H 65 GLN H 80 ASN H 82 ASN H 148 ASN H 149 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 19230 Z= 0.186 Angle : 0.743 14.402 26232 Z= 0.394 Chirality : 0.045 0.322 2972 Planarity : 0.004 0.042 3141 Dihedral : 12.271 152.234 3134 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.72 % Favored : 87.86 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.16), residues: 2167 helix: -1.68 (0.16), residues: 821 sheet: -2.23 (0.26), residues: 335 loop : -3.19 (0.17), residues: 1011 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 388 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 28 residues processed: 426 average time/residue: 0.3547 time to fit residues: 222.0901 Evaluate side-chains 332 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 304 time to evaluate : 1.921 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 28 outliers final: 1 residues processed: 28 average time/residue: 0.1825 time to fit residues: 12.3818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 218 optimal weight: 7.9990 chunk 179 optimal weight: 0.7980 chunk 200 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 78 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN F 11 GLN G 104 GLN H 148 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 19230 Z= 0.190 Angle : 0.686 13.069 26232 Z= 0.364 Chirality : 0.044 0.311 2972 Planarity : 0.004 0.035 3141 Dihedral : 11.768 152.817 3134 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.41 % Favored : 87.31 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.94 (0.17), residues: 2167 helix: -0.81 (0.17), residues: 831 sheet: -1.88 (0.27), residues: 335 loop : -3.01 (0.17), residues: 1001 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 333 time to evaluate : 2.303 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 18 residues processed: 365 average time/residue: 0.3657 time to fit residues: 195.7511 Evaluate side-chains 297 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 279 time to evaluate : 2.174 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.2036 time to fit residues: 9.4628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 192 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 434 HIS ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN A 661 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN C 26 ASN D 85 ASN F 11 GLN G 125 HIS ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 19230 Z= 0.296 Angle : 0.733 13.491 26232 Z= 0.389 Chirality : 0.046 0.304 2972 Planarity : 0.004 0.042 3141 Dihedral : 11.716 149.667 3134 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.46 % Favored : 87.22 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.60 (0.17), residues: 2167 helix: -0.46 (0.18), residues: 832 sheet: -1.68 (0.26), residues: 337 loop : -2.90 (0.18), residues: 998 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 312 time to evaluate : 1.972 Fit side-chains outliers start: 54 outliers final: 35 residues processed: 346 average time/residue: 0.3578 time to fit residues: 181.0266 Evaluate side-chains 318 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 283 time to evaluate : 2.167 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 1 residues processed: 35 average time/residue: 0.2311 time to fit residues: 16.4680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN C 72 GLN F 11 GLN G 167 ASN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 19230 Z= 0.414 Angle : 0.807 14.244 26232 Z= 0.427 Chirality : 0.050 0.328 2972 Planarity : 0.005 0.052 3141 Dihedral : 11.822 150.113 3134 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.06 % Favored : 86.53 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.38 % 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: -2.55 (0.17), residues: 2167 helix: -0.50 (0.17), residues: 836 sheet: -1.48 (0.27), residues: 316 loop : -2.85 (0.18), residues: 1015 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 300 time to evaluate : 2.224 Fit side-chains outliers start: 51 outliers final: 28 residues processed: 333 average time/residue: 0.3434 time to fit residues: 169.4657 Evaluate side-chains 303 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 275 time to evaluate : 1.919 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2068 time to fit residues: 12.4938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 0.3980 chunk 193 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 125 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 297 ASN A 414 HIS ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN F 11 GLN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 19230 Z= 0.190 Angle : 0.662 13.069 26232 Z= 0.352 Chirality : 0.043 0.312 2972 Planarity : 0.004 0.041 3141 Dihedral : 11.592 149.241 3134 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.09 % Favored : 87.59 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.16 (0.18), residues: 2167 helix: -0.02 (0.18), residues: 832 sheet: -1.42 (0.27), residues: 326 loop : -2.72 (0.18), residues: 1009 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 313 time to evaluate : 2.197 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 329 average time/residue: 0.3768 time to fit residues: 183.4960 Evaluate side-chains 291 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 276 time to evaluate : 2.043 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2635 time to fit residues: 10.1753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 122 optimal weight: 0.3980 chunk 156 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 213 optimal weight: 8.9990 chunk 133 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 414 HIS ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN F 11 GLN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 ASN H 22 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19230 Z= 0.194 Angle : 0.653 13.150 26232 Z= 0.348 Chirality : 0.043 0.306 2972 Planarity : 0.004 0.034 3141 Dihedral : 11.411 149.600 3134 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.41 % Favored : 87.26 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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 (0.18), residues: 2167 helix: 0.21 (0.18), residues: 833 sheet: -1.20 (0.28), residues: 324 loop : -2.68 (0.18), residues: 1010 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 300 time to evaluate : 2.197 Fit side-chains outliers start: 28 outliers final: 11 residues processed: 317 average time/residue: 0.3557 time to fit residues: 166.5741 Evaluate side-chains 283 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 272 time to evaluate : 2.072 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1801 time to fit residues: 6.4936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN F 11 GLN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 19230 Z= 0.324 Angle : 0.729 13.420 26232 Z= 0.387 Chirality : 0.046 0.305 2972 Planarity : 0.004 0.063 3141 Dihedral : 11.491 150.193 3134 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.69 % Favored : 86.99 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.99 (0.18), residues: 2167 helix: 0.11 (0.18), residues: 830 sheet: -1.18 (0.28), residues: 316 loop : -2.65 (0.18), residues: 1021 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 272 time to evaluate : 2.078 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 284 average time/residue: 0.3560 time to fit residues: 150.3154 Evaluate side-chains 276 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 262 time to evaluate : 2.080 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1729 time to fit residues: 7.2537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.0170 chunk 204 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 188 optimal weight: 0.2980 chunk 198 optimal weight: 0.0270 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 175 ASN A 297 ASN A 598 ASN A 604 ASN D 144 ASN F 11 GLN G 134 ASN G 161 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 19230 Z= 0.152 Angle : 0.630 12.259 26232 Z= 0.334 Chirality : 0.042 0.320 2972 Planarity : 0.004 0.045 3141 Dihedral : 11.298 149.794 3134 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.68 % Favored : 88.05 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.71 (0.18), residues: 2167 helix: 0.59 (0.18), residues: 824 sheet: -1.14 (0.28), residues: 324 loop : -2.69 (0.18), residues: 1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 306 time to evaluate : 2.867 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 314 average time/residue: 0.3674 time to fit residues: 172.6055 Evaluate side-chains 273 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 267 time to evaluate : 2.054 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1867 time to fit residues: 4.8877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 100 optimal weight: 0.2980 chunk 146 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 203 optimal weight: 0.0770 chunk 176 optimal weight: 5.9990 chunk 18 optimal weight: 0.0060 chunk 136 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.6756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 26 ASN G 55 GLN G 161 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 19230 Z= 0.156 Angle : 0.623 14.039 26232 Z= 0.328 Chirality : 0.042 0.303 2972 Planarity : 0.003 0.035 3141 Dihedral : 11.117 149.836 3134 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.44 % Favored : 88.28 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.56 (0.18), residues: 2167 helix: 0.75 (0.19), residues: 829 sheet: -1.09 (0.28), residues: 334 loop : -2.66 (0.18), residues: 1004 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 291 time to evaluate : 1.940 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 296 average time/residue: 0.3557 time to fit residues: 155.1870 Evaluate side-chains 277 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 274 time to evaluate : 1.696 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1659 time to fit residues: 3.6139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.0570 chunk 187 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 112 ASN G 134 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.167069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.146427 restraints weight = 24814.147| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.53 r_work: 0.3482 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19230 Z= 0.168 Angle : 0.629 13.423 26232 Z= 0.331 Chirality : 0.042 0.304 2972 Planarity : 0.004 0.040 3141 Dihedral : 11.043 150.302 3134 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.54 % Favored : 88.19 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.53 (0.18), residues: 2167 helix: 0.84 (0.18), residues: 833 sheet: -1.10 (0.28), residues: 334 loop : -2.70 (0.18), residues: 1000 =============================================================================== Job complete usr+sys time: 4305.26 seconds wall clock time: 78 minutes 45.06 seconds (4725.06 seconds total)