Starting phenix.real_space_refine (version: dev) on Tue Feb 21 07:32:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo1_14080/02_2023/7qo1_14080_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo1_14080/02_2023/7qo1_14080.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo1_14080/02_2023/7qo1_14080_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo1_14080/02_2023/7qo1_14080_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo1_14080/02_2023/7qo1_14080_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo1_14080/02_2023/7qo1_14080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo1_14080/02_2023/7qo1_14080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo1_14080/02_2023/7qo1_14080_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo1_14080/02_2023/7qo1_14080_neut_updated.pdb" } resolution = 4.4 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= 0.001 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 294": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 435": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 515": "NH1" <-> "NH2" Residue "A ARG 527": "NH1" <-> "NH2" Residue "A ARG 549": "NH1" <-> "NH2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A ARG 573": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 677": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 683": "NH1" <-> "NH2" Residue "A ARG 738": "NH1" <-> "NH2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A ARG 771": "NH1" <-> "NH2" Residue "A ARG 774": "NH1" <-> "NH2" Residue "A ARG 821": "NH1" <-> "NH2" Residue "A ARG 825": "NH1" <-> "NH2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A ARG 874": "NH1" <-> "NH2" Residue "A ARG 877": "NH1" <-> "NH2" Residue "A ARG 879": "NH1" <-> "NH2" Residue "A ARG 898": "NH1" <-> "NH2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "F ARG 5": "NH1" <-> "NH2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 61": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "G ARG 5": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 70": "NH1" <-> "NH2" Residue "Y ARG 73": "NH1" <-> "NH2" Residue "Y ARG 192": "NH1" <-> "NH2" Residue "Y ARG 211": "NH1" <-> "NH2" Residue "Y ARG 245": "NH1" <-> "NH2" Residue "Y ARG 261": "NH1" <-> "NH2" Residue "Y ARG 262": "NH1" <-> "NH2" Residue "Y ARG 320": "NH1" <-> "NH2" Residue "Y ARG 322": "NH1" <-> "NH2" Residue "Y ARG 327": "NH1" <-> "NH2" Residue "Y ARG 332": "NH1" <-> "NH2" 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: 14179 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 4960 Classifications: {'peptide': 640} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 600} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1930 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 247} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1925 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1873 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 387 Unusual residues: {'DOC': 1} Classifications: {'DNA': 18, 'undetermined': 1} Link IDs: {'rna3p': 17, None: 1} Not linked: pdbres=" DT H 18 " pdbres="DOC H 19 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "I" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 248 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "J" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 635 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "Y" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2198 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 15, 'TRANS': 285} Chain breaks: 2 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 92 Chain: "I" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 8.24, per 1000 atoms: 0.58 Number of scatterers: 14179 At special positions: 0 Unit cell: (120.24, 118.57, 134.435, 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 77 16.00 P 63 15.00 O 2875 8.00 N 2419 7.00 C 8745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.26 Conformation dependent library (CDL) restraints added in 1.9 seconds 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3188 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 16 sheets defined 31.6% alpha, 23.5% beta 27 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 4.90 Creating SS restraints... Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 305 through 322 Processing helix chain 'A' and resid 324 through 335 removed outlier: 4.126A pdb=" N LEU A 328 " --> pdb=" O PRO A 325 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 366 through 376 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 401 through 413 Processing helix chain 'A' and resid 419 through 432 Processing helix chain 'A' and resid 438 through 447 removed outlier: 3.749A pdb=" N SER A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 469 Processing helix chain 'A' and resid 489 through 509 Processing helix chain 'A' and resid 513 through 523 Proline residue: A 518 - end of helix Processing helix chain 'A' and resid 528 through 530 No H-bonds generated for 'chain 'A' and resid 528 through 530' Processing helix chain 'A' and resid 551 through 557 Processing helix chain 'A' and resid 599 through 608 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 635 through 640 removed outlier: 3.979A pdb=" N THR A 640 " --> pdb=" O GLN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 685 Processing helix chain 'A' and resid 704 through 716 Processing helix chain 'A' and resid 747 through 750 No H-bonds generated for 'chain 'A' and resid 747 through 750' Processing helix chain 'A' and resid 769 through 771 No H-bonds generated for 'chain 'A' and resid 769 through 771' Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 884 through 886 No H-bonds generated for 'chain 'A' and resid 884 through 886' Processing helix chain 'A' and resid 890 through 900 Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 54 through 56 No H-bonds generated for 'chain 'B' and resid 54 through 56' Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 141 through 153 removed outlier: 4.608A pdb=" N HIS B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 removed outlier: 4.349A pdb=" N LYS B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N THR B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Proline residue: B 220 - end of helix Processing helix chain 'F' and resid 9 through 19 removed outlier: 3.879A pdb=" N LEU F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 72 through 81 removed outlier: 4.592A pdb=" N CYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 154 removed outlier: 3.606A pdb=" N HIS F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 221 removed outlier: 4.936A pdb=" N LYS F 217 " --> pdb=" O ASN F 213 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA F 218 " --> pdb=" O PHE F 214 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N THR F 219 " --> pdb=" O PHE F 215 " (cutoff:3.500A) Proline residue: F 220 - end of helix Processing helix chain 'G' and resid 10 through 22 removed outlier: 4.797A pdb=" N ASP G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 56 No H-bonds generated for 'chain 'G' and resid 54 through 56' Processing helix chain 'G' and resid 72 through 79 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'G' and resid 209 through 221 removed outlier: 5.461A pdb=" N PHE G 214 " --> pdb=" O ARG G 210 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS G 217 " --> pdb=" O ASN G 213 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ALA G 218 " --> pdb=" O PHE G 214 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR G 219 " --> pdb=" O PHE G 215 " (cutoff:3.500A) Proline residue: G 220 - end of helix Processing helix chain 'Y' and resid 6 through 13 Processing helix chain 'Y' and resid 15 through 17 No H-bonds generated for 'chain 'Y' and resid 15 through 17' Processing helix chain 'Y' and resid 23 through 26 Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 61 through 77 removed outlier: 3.850A pdb=" N GLY Y 66 " --> pdb=" O HIS Y 63 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG Y 70 " --> pdb=" O MET Y 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 136 through 148 removed outlier: 3.797A pdb=" N LEU Y 144 " --> pdb=" O GLU Y 140 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER Y 146 " --> pdb=" O LYS Y 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 159 through 169 Processing helix chain 'Y' and resid 181 through 184 No H-bonds generated for 'chain 'Y' and resid 181 through 184' Processing helix chain 'Y' and resid 209 through 216 Processing helix chain 'Y' and resid 221 through 231 removed outlier: 4.926A pdb=" N LEU Y 226 " --> pdb=" O GLN Y 222 " (cutoff:3.500A) Processing helix chain 'Y' and resid 243 through 252 removed outlier: 3.950A pdb=" N VAL Y 247 " --> pdb=" O LYS Y 244 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU Y 249 " --> pdb=" O ALA Y 246 " (cutoff:3.500A) Processing helix chain 'Y' and resid 256 through 262 removed outlier: 3.518A pdb=" N ARG Y 261 " --> pdb=" O GLU Y 257 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG Y 262 " --> pdb=" O GLU Y 258 " (cutoff:3.500A) Processing helix chain 'Y' and resid 278 through 284 Processing helix chain 'Y' and resid 291 through 293 No H-bonds generated for 'chain 'Y' and resid 291 through 293' Processing helix chain 'Y' and resid 305 through 313 removed outlier: 3.852A pdb=" N PHE Y 309 " --> pdb=" O GLU Y 305 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS Y 311 " --> pdb=" O ILE Y 307 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY Y 312 " --> pdb=" O LYS Y 308 " (cutoff:3.500A) Processing helix chain 'Y' and resid 318 through 333 removed outlier: 3.618A pdb=" N ARG Y 332 " --> pdb=" O LEU Y 328 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN Y 333 " --> pdb=" O SER Y 329 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 343 No H-bonds generated for 'chain 'Y' and resid 340 through 343' Processing sheet with id= A, first strand: chain 'A' and resid 545 through 548 removed outlier: 7.452A pdb=" N TRP A 742 " --> pdb=" O HIS A 546 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR A 548 " --> pdb=" O TRP A 742 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LYS A 744 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY A 721 " --> pdb=" O LYS A 568 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 584 through 587 Processing sheet with id= C, first strand: chain 'A' and resid 789 through 796 removed outlier: 7.057A pdb=" N LEU A 780 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS A 795 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE A 778 " --> pdb=" O LYS A 795 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA A 781 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL A 761 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N TYR A 783 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N LEU A 759 " --> pdb=" O TYR A 783 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL A 841 " --> pdb=" O ARG A 879 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LYS A 845 " --> pdb=" O PHE A 875 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE A 875 " --> pdb=" O LYS A 845 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 848 through 850 removed outlier: 3.596A pdb=" N ASP A 848 " --> pdb=" O ARG A 871 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 616 through 619 removed outlier: 6.480A pdb=" N ASP A 619 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU A 662 " --> pdb=" O ASP A 619 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 59 through 62 Processing sheet with id= G, first strand: chain 'B' and resid 66 through 71 removed outlier: 7.599A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LYS B 240 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR B 224 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 203 through 208 removed outlier: 4.003A pdb=" N VAL B 203 " --> pdb=" O CYS B 162 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 59 through 62 Processing sheet with id= J, first strand: chain 'F' and resid 66 through 71 removed outlier: 8.109A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 203 through 208 removed outlier: 5.780A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 59 through 62 removed outlier: 4.046A pdb=" N THR G 59 " --> pdb=" O ARG G 5 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 66 through 71 removed outlier: 8.211A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 203 through 208 removed outlier: 5.590A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'Y' and resid 18 through 21 Processing sheet with id= P, first strand: chain 'Y' and resid 174 through 176 removed outlier: 3.698A pdb=" N ALA Y 174 " --> pdb=" O LYS Y 30 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS Y 80 " --> pdb=" O VAL Y 31 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE Y 33 " --> pdb=" O LYS Y 80 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL Y 82 " --> pdb=" O ILE Y 33 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 6.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2597 1.31 - 1.44: 3587 1.44 - 1.57: 8117 1.57 - 1.70: 122 1.70 - 1.83: 121 Bond restraints: 14544 Sorted by residual: bond pdb=" O3' DG H 17 " pdb=" P DT H 18 " ideal model delta sigma weight residual 1.607 1.479 0.128 1.50e-02 4.44e+03 7.24e+01 bond pdb=" C5 AMP I 100 " pdb=" C6 AMP I 100 " ideal model delta sigma weight residual 1.490 1.345 0.145 2.00e-02 2.50e+03 5.29e+01 bond pdb=" C4 AMP I 100 " pdb=" C5 AMP I 100 " ideal model delta sigma weight residual 1.490 1.374 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" O1P AMP I 100 " pdb=" P AMP I 100 " ideal model delta sigma weight residual 1.510 1.418 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C6 AMP I 100 " pdb=" N6 AMP I 100 " ideal model delta sigma weight residual 1.355 1.435 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 14539 not shown) Histogram of bond angle deviations from ideal: 97.14 - 105.33: 535 105.33 - 113.52: 7690 113.52 - 121.71: 8164 121.71 - 129.90: 3505 129.90 - 138.09: 64 Bond angle restraints: 19958 Sorted by residual: angle pdb=" CA PHE Y 42 " pdb=" CB PHE Y 42 " pdb=" CG PHE Y 42 " ideal model delta sigma weight residual 113.80 121.03 -7.23 1.00e+00 1.00e+00 5.23e+01 angle pdb=" CA PHE G 57 " pdb=" CB PHE G 57 " pdb=" CG PHE G 57 " ideal model delta sigma weight residual 113.80 120.43 -6.63 1.00e+00 1.00e+00 4.40e+01 angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DT I 21 " ideal model delta sigma weight residual 120.20 110.42 9.78 1.50e+00 4.44e-01 4.25e+01 angle pdb=" C LYS A 585 " pdb=" N ILE A 586 " pdb=" CA ILE A 586 " ideal model delta sigma weight residual 122.99 131.52 -8.53 1.39e+00 5.18e-01 3.77e+01 angle pdb=" N MET G 139 " pdb=" CA MET G 139 " pdb=" C MET G 139 " ideal model delta sigma weight residual 108.22 113.65 -5.43 9.00e-01 1.23e+00 3.65e+01 ... (remaining 19953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.52: 8082 29.52 - 59.04: 507 59.04 - 88.56: 63 88.56 - 118.08: 2 118.08 - 147.60: 1 Dihedral angle restraints: 8655 sinusoidal: 3738 harmonic: 4917 Sorted by residual: dihedral pdb=" C2' AMP I 100 " pdb=" C1' AMP I 100 " pdb=" N9 AMP I 100 " pdb=" C4 AMP I 100 " ideal model delta sinusoidal sigma weight residual 91.55 -56.04 147.60 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" C5' AMP I 100 " pdb=" O5' AMP I 100 " pdb=" P AMP I 100 " pdb=" O3P AMP I 100 " ideal model delta sinusoidal sigma weight residual -60.00 -167.65 107.65 1 2.00e+01 2.50e-03 3.13e+01 dihedral pdb=" CA LEU Y 202 " pdb=" C LEU Y 202 " pdb=" N PRO Y 203 " pdb=" CA PRO Y 203 " ideal model delta harmonic sigma weight residual 180.00 152.33 27.67 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 8652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2141 0.156 - 0.311: 165 0.311 - 0.467: 7 0.467 - 0.623: 0 0.623 - 0.778: 1 Chirality restraints: 2314 Sorted by residual: chirality pdb=" P DG I 20 " pdb=" OP1 DG I 20 " pdb=" OP2 DG I 20 " pdb=" O5' DG I 20 " both_signs ideal model delta sigma weight residual True 2.35 -3.12 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" P DT I 21 " pdb=" OP1 DT I 21 " pdb=" OP2 DT I 21 " pdb=" O5' DT I 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CA PRO A 838 " pdb=" N PRO A 838 " pdb=" C PRO A 838 " pdb=" CB PRO A 838 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.14e+00 ... (remaining 2311 not shown) Planarity restraints: 2362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 27 " 0.206 2.00e-02 2.50e+03 1.19e-01 3.57e+02 pdb=" N1 DT I 27 " 0.025 2.00e-02 2.50e+03 pdb=" C2 DT I 27 " -0.029 2.00e-02 2.50e+03 pdb=" O2 DT I 27 " -0.230 2.00e-02 2.50e+03 pdb=" N3 DT I 27 " 0.095 2.00e-02 2.50e+03 pdb=" C4 DT I 27 " 0.071 2.00e-02 2.50e+03 pdb=" O4 DT I 27 " 0.101 2.00e-02 2.50e+03 pdb=" C5 DT I 27 " -0.040 2.00e-02 2.50e+03 pdb=" C7 DT I 27 " -0.114 2.00e-02 2.50e+03 pdb=" C6 DT I 27 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J 2 " 0.170 2.00e-02 2.50e+03 1.14e-01 3.26e+02 pdb=" N1 DT J 2 " 0.050 2.00e-02 2.50e+03 pdb=" C2 DT J 2 " -0.040 2.00e-02 2.50e+03 pdb=" O2 DT J 2 " -0.216 2.00e-02 2.50e+03 pdb=" N3 DT J 2 " 0.047 2.00e-02 2.50e+03 pdb=" C4 DT J 2 " 0.053 2.00e-02 2.50e+03 pdb=" O4 DT J 2 " 0.142 2.00e-02 2.50e+03 pdb=" C5 DT J 2 " -0.040 2.00e-02 2.50e+03 pdb=" C7 DT J 2 " -0.154 2.00e-02 2.50e+03 pdb=" C6 DT J 2 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT H 8 " 0.149 2.00e-02 2.50e+03 1.07e-01 2.87e+02 pdb=" N1 DT H 8 " 0.089 2.00e-02 2.50e+03 pdb=" C2 DT H 8 " -0.044 2.00e-02 2.50e+03 pdb=" O2 DT H 8 " -0.141 2.00e-02 2.50e+03 pdb=" N3 DT H 8 " -0.075 2.00e-02 2.50e+03 pdb=" C4 DT H 8 " 0.028 2.00e-02 2.50e+03 pdb=" O4 DT H 8 " 0.195 2.00e-02 2.50e+03 pdb=" C5 DT H 8 " -0.044 2.00e-02 2.50e+03 pdb=" C7 DT H 8 " -0.125 2.00e-02 2.50e+03 pdb=" C6 DT H 8 " -0.032 2.00e-02 2.50e+03 ... (remaining 2359 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3664 2.85 - 3.36: 14021 3.36 - 3.87: 23764 3.87 - 4.39: 27034 4.39 - 4.90: 44020 Nonbonded interactions: 112503 Sorted by model distance: nonbonded pdb=" NZ LYS A 744 " pdb=" O3P AMP I 100 " model vdw 2.337 2.520 nonbonded pdb=" OD2 ASP B 41 " pdb=" OG SER B 43 " model vdw 2.415 2.440 nonbonded pdb=" O ASP Y 290 " pdb=" OG SER Y 293 " model vdw 2.438 2.440 nonbonded pdb=" O ASP A 600 " pdb=" OG SER A 603 " model vdw 2.472 2.440 nonbonded pdb=" O2 DT H 8 " pdb=" N1 DA J 24 " model vdw 2.481 2.496 ... (remaining 112498 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' and (resid 1 through 63 or (resid 64 and (name N or name CA or name C \ or name O or name CB )) or resid 65 through 173 or (resid 174 and (name N or na \ me CA or name C or name O or name CB )) or resid 175 through 185 or resid 195 th \ rough 209 or (resid 210 and (name N or name CA or name C or name O or name CB )) \ or resid 211 through 255)) selection = (chain 'F' and (resid 1 through 63 or (resid 64 and (name N or name CA or name C \ or name O or name CB )) or resid 65 through 121 or (resid 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 137 or (resid 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 173 \ or (resid 174 and (name N or name CA or name C or name O or name CB )) or resid \ 175 through 180 or (resid 181 and (name N or name CA or name C or name O or nam \ e CB )) or resid 182 through 185 or resid 195 through 209 or (resid 210 and (nam \ e N or name CA or name C or name O or name CB )) or resid 211 through 239 or (re \ sid 240 and (name N or name CA or name C or name O or name CB )) or resid 241 th \ rough 255)) selection = (chain 'G' and (resid 1 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 or (resid 109 and (name N or name CA or \ name C or name O or name CB )) or resid 110 through 121 or (resid 122 and (name \ N or name CA or name C or name O or name CB )) or resid 123 through 163 or (resi \ d 164 and (name N or name CA or name C or name O or name CB )) or resid 165 thro \ ugh 180 or (resid 181 and (name N or name CA or name C or name O or name CB )) o \ r resid 182 through 239 or (resid 240 and (name N or name CA or name C or name O \ or name CB )) or resid 241 through 255)) } 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 63 5.49 5 S 77 5.16 5 C 8745 2.51 5 N 2419 2.21 5 O 2875 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 4.850 Check model and map are aligned: 0.220 Process input model: 42.630 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 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 0.145 14544 Z= 0.785 Angle : 1.847 13.323 19958 Z= 1.195 Chirality : 0.090 0.778 2314 Planarity : 0.018 0.218 2362 Dihedral : 18.305 147.598 5467 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.25 % Favored : 94.57 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.19), residues: 1676 helix: -1.86 (0.19), residues: 465 sheet: -0.02 (0.25), residues: 389 loop : -1.33 (0.21), residues: 822 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 265 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 2 residues processed: 282 average time/residue: 0.2962 time to fit residues: 120.0836 Evaluate side-chains 172 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 2.059 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1867 time to fit residues: 3.0217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 135 optimal weight: 0.0000 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 436 HIS ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN G 38 GLN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 138 ASN Y 193 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 14544 Z= 0.184 Angle : 0.660 7.422 19958 Z= 0.353 Chirality : 0.043 0.185 2314 Planarity : 0.004 0.062 2362 Dihedral : 18.376 145.793 2415 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -0.63 (0.20), residues: 1676 helix: -0.03 (0.23), residues: 478 sheet: 0.27 (0.24), residues: 448 loop : -1.04 (0.22), residues: 750 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.2701 time to fit residues: 90.8760 Evaluate side-chains 164 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN F 108 GLN F 200 ASN Y 41 GLN Y 63 HIS Y 193 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.146 14544 Z= 0.475 Angle : 0.929 14.821 19958 Z= 0.482 Chirality : 0.051 0.221 2314 Planarity : 0.006 0.077 2362 Dihedral : 19.272 148.002 2415 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.19), residues: 1676 helix: -0.96 (0.22), residues: 470 sheet: -0.22 (0.24), residues: 436 loop : -1.63 (0.21), residues: 770 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 200 time to evaluate : 1.752 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 206 average time/residue: 0.2507 time to fit residues: 78.4555 Evaluate side-chains 159 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 1.734 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1400 time to fit residues: 3.6025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 149 optimal weight: 0.7980 chunk 45 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN A 272 ASN A 314 ASN A 436 HIS ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS F 184 GLN Y 193 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 14544 Z= 0.171 Angle : 0.639 7.970 19958 Z= 0.331 Chirality : 0.043 0.205 2314 Planarity : 0.004 0.052 2362 Dihedral : 18.705 140.999 2415 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -0.99 (0.20), residues: 1676 helix: -0.10 (0.23), residues: 481 sheet: -0.06 (0.23), residues: 453 loop : -1.36 (0.22), residues: 742 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 1.499 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.2552 time to fit residues: 87.2765 Evaluate side-chains 166 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.728 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 GLN Y 63 HIS Y 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 14544 Z= 0.297 Angle : 0.734 13.002 19958 Z= 0.377 Chirality : 0.045 0.231 2314 Planarity : 0.005 0.065 2362 Dihedral : 18.867 137.875 2415 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.20), residues: 1676 helix: -0.29 (0.23), residues: 479 sheet: -0.20 (0.23), residues: 456 loop : -1.53 (0.22), residues: 741 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2466 time to fit residues: 76.2716 Evaluate side-chains 161 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.599 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 0.2980 chunk 87 optimal weight: 5.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 523 HIS ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 14544 Z= 0.302 Angle : 0.748 14.157 19958 Z= 0.386 Chirality : 0.046 0.205 2314 Planarity : 0.005 0.056 2362 Dihedral : 19.069 139.755 2415 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.20), residues: 1676 helix: -0.46 (0.23), residues: 476 sheet: -0.42 (0.24), residues: 445 loop : -1.68 (0.21), residues: 755 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 212 average time/residue: 0.2523 time to fit residues: 80.5037 Evaluate side-chains 161 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1282 time to fit residues: 2.3261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 436 HIS ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 14544 Z= 0.293 Angle : 0.737 16.099 19958 Z= 0.379 Chirality : 0.046 0.202 2314 Planarity : 0.005 0.056 2362 Dihedral : 19.082 137.970 2415 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.19), residues: 1676 helix: -0.37 (0.23), residues: 463 sheet: -0.51 (0.24), residues: 427 loop : -1.69 (0.21), residues: 786 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2408 time to fit residues: 77.6797 Evaluate side-chains 158 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 575 GLN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 91 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 14544 Z= 0.345 Angle : 0.815 18.864 19958 Z= 0.418 Chirality : 0.048 0.197 2314 Planarity : 0.006 0.075 2362 Dihedral : 19.163 138.769 2415 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.19), residues: 1676 helix: -0.71 (0.23), residues: 468 sheet: -0.64 (0.25), residues: 408 loop : -1.81 (0.21), residues: 800 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2494 time to fit residues: 78.5932 Evaluate side-chains 157 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.641 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 155 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 436 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 HIS G 24 ASN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 GLN Y 253 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 14544 Z= 0.311 Angle : 0.778 17.186 19958 Z= 0.400 Chirality : 0.047 0.226 2314 Planarity : 0.005 0.072 2362 Dihedral : 19.026 138.080 2415 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.19), residues: 1676 helix: -0.64 (0.23), residues: 468 sheet: -0.64 (0.25), residues: 399 loop : -1.81 (0.21), residues: 809 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2536 time to fit residues: 78.1567 Evaluate side-chains 150 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.750 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 106 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 436 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN A 685 ASN G 24 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 GLN Y 253 HIS ** Y 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 14544 Z= 0.180 Angle : 0.657 10.096 19958 Z= 0.337 Chirality : 0.043 0.217 2314 Planarity : 0.004 0.065 2362 Dihedral : 18.542 138.111 2415 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.20), residues: 1676 helix: 0.02 (0.24), residues: 470 sheet: -0.57 (0.24), residues: 432 loop : -1.62 (0.21), residues: 774 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2686 time to fit residues: 87.3416 Evaluate side-chains 167 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.676 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 137 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN G 24 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.102357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.087345 restraints weight = 66804.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.089572 restraints weight = 41363.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.091141 restraints weight = 29040.823| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14544 Z= 0.205 Angle : 0.676 13.399 19958 Z= 0.345 Chirality : 0.043 0.184 2314 Planarity : 0.005 0.061 2362 Dihedral : 18.517 137.942 2415 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1676 helix: 0.00 (0.24), residues: 464 sheet: -0.52 (0.25), residues: 423 loop : -1.55 (0.21), residues: 789 =============================================================================== Job complete usr+sys time: 2625.16 seconds wall clock time: 49 minutes 2.34 seconds (2942.34 seconds total)