Starting phenix.real_space_refine (version: dev) on Mon Feb 20 10:53:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppr_20446/02_2023/6ppr_20446_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppr_20446/02_2023/6ppr_20446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppr_20446/02_2023/6ppr_20446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppr_20446/02_2023/6ppr_20446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppr_20446/02_2023/6ppr_20446_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppr_20446/02_2023/6ppr_20446_neut_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 437": "NH1" <-> "NH2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "B ARG 614": "NH1" <-> "NH2" Residue "B ARG 683": "NH1" <-> "NH2" Residue "B PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 692": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 751": "NH1" <-> "NH2" Residue "B ARG 780": "NH1" <-> "NH2" Residue "B ARG 822": "NH1" <-> "NH2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ARG 670": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 681": "NH1" <-> "NH2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A ARG 751": "NH1" <-> "NH2" Residue "A ARG 760": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A ARG 873": "NH1" <-> "NH2" Residue "A ARG 914": "NH1" <-> "NH2" Residue "A ASP 920": "OD1" <-> "OD2" Residue "A ARG 990": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1033": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11995 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5558 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 44, 'TRANS': 715} Chain breaks: 14 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 14, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 20, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 178 Chain: "A" Number of atoms: 5746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 5746 Classifications: {'peptide': 834} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 47, 'TRANS': 786} Chain breaks: 22 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 559 Unresolved non-hydrogen angles: 701 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 25, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 3, 'GLU:plan': 34, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 417 Chain: "X" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'ANP': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.19, per 1000 atoms: 0.60 Number of scatterers: 11995 At special positions: 0 Unit cell: (142.976, 93.0204, 105.079, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 40 16.00 P 35 15.00 O 2223 8.00 N 2210 7.00 C 7483 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: 5.00 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1102 " pdb="FE4 SF4 A1102 " - pdb=" SG CYS A 807 " pdb="FE2 SF4 A1102 " - pdb=" SG CYS A1036 " pdb="FE1 SF4 A1102 " - pdb=" SG CYS A1030 " pdb="FE3 SF4 A1102 " - pdb=" SG CYS A1027 " Number of angles added : 12 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 7 sheets defined 38.3% alpha, 4.6% beta 3 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'B' and resid 54 through 60 removed outlier: 3.819A pdb=" N ALA B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 82 through 96 removed outlier: 4.230A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 removed outlier: 3.751A pdb=" N GLY B 124 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 4.001A pdb=" N ASP B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 removed outlier: 4.048A pdb=" N GLY B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.866A pdb=" N HIS B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 205' Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.614A pdb=" N THR B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 229 " --> pdb=" O MET B 225 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 removed outlier: 3.853A pdb=" N ALA B 241 " --> pdb=" O PRO B 237 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 4.131A pdb=" N MET B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.526A pdb=" N ALA B 369 " --> pdb=" O HIS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.075A pdb=" N ASP B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS B 413 " --> pdb=" O TRP B 409 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.562A pdb=" N ALA B 442 " --> pdb=" O ASN B 438 " (cutoff:3.500A) Proline residue: B 443 - end of helix No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 470 through 473 No H-bonds generated for 'chain 'B' and resid 470 through 473' Processing helix chain 'B' and resid 477 through 480 No H-bonds generated for 'chain 'B' and resid 477 through 480' Processing helix chain 'B' and resid 489 through 492 No H-bonds generated for 'chain 'B' and resid 489 through 492' Processing helix chain 'B' and resid 501 through 513 removed outlier: 4.146A pdb=" N ARG B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 513 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 527 No H-bonds generated for 'chain 'B' and resid 524 through 527' Processing helix chain 'B' and resid 555 through 571 removed outlier: 3.945A pdb=" N GLU B 559 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 563 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET B 570 " --> pdb=" O ARG B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 589 removed outlier: 3.802A pdb=" N ALA B 584 " --> pdb=" O PRO B 580 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU B 585 " --> pdb=" O GLU B 581 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 604 No H-bonds generated for 'chain 'B' and resid 602 through 604' Processing helix chain 'B' and resid 610 through 622 removed outlier: 4.136A pdb=" N PHE B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 618 " --> pdb=" O ARG B 614 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP B 621 " --> pdb=" O ASP B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 643 removed outlier: 3.703A pdb=" N GLU B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 758 removed outlier: 3.502A pdb=" N SER B 732 " --> pdb=" O ARG B 728 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP B 733 " --> pdb=" O LYS B 729 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS B 740 " --> pdb=" O SER B 736 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP B 743 " --> pdb=" O LYS B 739 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 749 " --> pdb=" O ARG B 745 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 750 " --> pdb=" O ARG B 746 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 752 " --> pdb=" O ASP B 748 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 753 " --> pdb=" O GLU B 749 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 756 " --> pdb=" O ARG B 752 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 794 removed outlier: 4.274A pdb=" N THR B 791 " --> pdb=" O CYS B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 850 removed outlier: 3.810A pdb=" N GLN B 845 " --> pdb=" O HIS B 841 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 847 " --> pdb=" O GLY B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 875 removed outlier: 3.834A pdb=" N ALA B 873 " --> pdb=" O ASP B 869 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU B 874 " --> pdb=" O ALA B 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.636A pdb=" N ARG A 70 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 98 through 101 No H-bonds generated for 'chain 'A' and resid 98 through 101' Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.979A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.674A pdb=" N ARG A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.680A pdb=" N GLN A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 175 through 179' Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.710A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.668A pdb=" N GLU A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.744A pdb=" N ASN A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 removed outlier: 4.027A pdb=" N LEU A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 3.570A pdb=" N ALA A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 removed outlier: 3.800A pdb=" N ILE A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 401 removed outlier: 3.806A pdb=" N ALA A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 434 removed outlier: 3.781A pdb=" N THR A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 446 removed outlier: 4.117A pdb=" N ALA A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 446' Processing helix chain 'A' and resid 458 through 465 removed outlier: 3.795A pdb=" N ARG A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 485 removed outlier: 3.592A pdb=" N VAL A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 504 removed outlier: 4.145A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 No H-bonds generated for 'chain 'A' and resid 506 through 509' Processing helix chain 'A' and resid 520 through 530 removed outlier: 3.724A pdb=" N LEU A 524 " --> pdb=" O ARG A 521 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N TRP A 525 " --> pdb=" O TYR A 522 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS A 529 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 530 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 547 through 566 removed outlier: 3.824A pdb=" N THR A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 641 through 647 removed outlier: 3.834A pdb=" N ASP A 646 " --> pdb=" O GLN A 642 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 647 " --> pdb=" O HIS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 679 removed outlier: 3.848A pdb=" N ARG A 671 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 673 " --> pdb=" O GLU A 669 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARG A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 708 No H-bonds generated for 'chain 'A' and resid 705 through 708' Processing helix chain 'A' and resid 728 through 738 removed outlier: 4.018A pdb=" N VAL A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 736 " --> pdb=" O VAL A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 762 removed outlier: 3.680A pdb=" N ALA A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 757 " --> pdb=" O CYS A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 808 through 814 Processing helix chain 'A' and resid 824 through 829 removed outlier: 3.611A pdb=" N GLY A 829 " --> pdb=" O ARG A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 836 Processing helix chain 'A' and resid 843 through 851 removed outlier: 3.720A pdb=" N VAL A 847 " --> pdb=" O GLU A 843 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 856 No H-bonds generated for 'chain 'A' and resid 854 through 856' Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.703A pdb=" N LEU A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 871 " --> pdb=" O ASN A 867 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 874 " --> pdb=" O ALA A 870 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 875 " --> pdb=" O ARG A 871 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A 879 " --> pdb=" O MET A 875 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 960 removed outlier: 3.918A pdb=" N LEU A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1014 removed outlier: 4.218A pdb=" N THR A1006 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A1012 " --> pdb=" O GLY A1008 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A1013 " --> pdb=" O GLU A1009 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1029 No H-bonds generated for 'chain 'A' and resid 1027 through 1029' Processing sheet with id= A, first strand: chain 'B' and resid 349 through 351 removed outlier: 6.371A pdb=" N LEU B 312 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL B 44 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA B 314 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR B 115 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR B 78 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER B 117 " --> pdb=" O THR B 78 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 675 through 677 Processing sheet with id= C, first strand: chain 'A' and resid 25 through 27 No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 348 through 353 removed outlier: 3.596A pdb=" N ALA A 688 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 619 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA A 604 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL A 386 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU A 606 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 794 through 796 Processing sheet with id= F, first strand: chain 'A' and resid 974 through 978 removed outlier: 3.894A pdb=" N THR A 988 " --> pdb=" O TYR A 978 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 892 through 895 removed outlier: 7.412A pdb=" N LEU A 922 " --> pdb=" O VAL A 893 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 6 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 3.75 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 4966 1.42 - 1.64: 7232 1.64 - 1.85: 58 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 12268 Sorted by residual: bond pdb=" N3B ANP A1101 " pdb=" PG ANP A1101 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O3A ANP A1101 " pdb=" PB ANP A1101 " ideal model delta sigma weight residual 1.700 1.601 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" N ARG B 385 " pdb=" CA ARG B 385 " ideal model delta sigma weight residual 1.453 1.488 -0.034 8.30e-03 1.45e+04 1.72e+01 bond pdb=" N VAL A 904 " pdb=" CA VAL A 904 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" N GLU B 352 " pdb=" CA GLU B 352 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.18e-02 7.18e+03 9.71e+00 ... (remaining 12263 not shown) Histogram of bond angle deviations from ideal: 73.49 - 85.65: 12 85.65 - 97.81: 1 97.81 - 109.96: 2960 109.96 - 122.12: 11444 122.12 - 134.28: 2494 Bond angle restraints: 16911 Sorted by residual: angle pdb=" N PRO B 208 " pdb=" CA PRO B 208 " pdb=" CB PRO B 208 " ideal model delta sigma weight residual 103.25 111.33 -8.08 1.05e+00 9.07e-01 5.92e+01 angle pdb=" N PRO B 211 " pdb=" CA PRO B 211 " pdb=" CB PRO B 211 " ideal model delta sigma weight residual 103.00 110.34 -7.34 1.10e+00 8.26e-01 4.45e+01 angle pdb=" N VAL B 756 " pdb=" CA VAL B 756 " pdb=" C VAL B 756 " ideal model delta sigma weight residual 112.29 107.04 5.25 9.40e-01 1.13e+00 3.12e+01 angle pdb=" C4' DC X 5 " pdb=" C3' DC X 5 " pdb=" O3' DC X 5 " ideal model delta sigma weight residual 110.00 117.53 -7.53 1.50e+00 4.44e-01 2.52e+01 angle pdb=" C4' DG X 12 " pdb=" C3' DG X 12 " pdb=" O3' DG X 12 " ideal model delta sigma weight residual 110.00 117.06 -7.06 1.50e+00 4.44e-01 2.22e+01 ... (remaining 16906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 6984 35.43 - 70.87: 148 70.87 - 106.30: 5 106.30 - 141.73: 0 141.73 - 177.17: 6 Dihedral angle restraints: 7143 sinusoidal: 2617 harmonic: 4526 Sorted by residual: dihedral pdb=" CA LEU B 134 " pdb=" C LEU B 134 " pdb=" N PRO B 135 " pdb=" CA PRO B 135 " ideal model delta harmonic sigma weight residual -180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA TYR A 859 " pdb=" C TYR A 859 " pdb=" N ASP A 860 " pdb=" CA ASP A 860 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA GLU A 814 " pdb=" C GLU A 814 " pdb=" N ARG A 815 " pdb=" CA ARG A 815 " ideal model delta harmonic sigma weight residual 180.00 151.68 28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 7140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1831 0.099 - 0.198: 214 0.198 - 0.297: 13 0.297 - 0.396: 1 0.396 - 0.495: 1 Chirality restraints: 2060 Sorted by residual: chirality pdb=" C3' DC X 5 " pdb=" C4' DC X 5 " pdb=" O3' DC X 5 " pdb=" C2' DC X 5 " both_signs ideal model delta sigma weight residual False -2.66 -2.17 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" C3' DG X 12 " pdb=" C4' DG X 12 " pdb=" O3' DG X 12 " pdb=" C2' DG X 12 " both_signs ideal model delta sigma weight residual False -2.66 -2.32 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C3' ANP A1101 " pdb=" C2' ANP A1101 " pdb=" C4' ANP A1101 " pdb=" O3' ANP A1101 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2057 not shown) Planarity restraints: 2053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 261 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ALA B 261 " 0.061 2.00e-02 2.50e+03 pdb=" O ALA B 261 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA B 262 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 348 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO B 349 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 349 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 349 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 807 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO A 808 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 808 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 808 " -0.041 5.00e-02 4.00e+02 ... (remaining 2050 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 86 2.61 - 3.18: 9361 3.18 - 3.75: 17061 3.75 - 4.33: 23253 4.33 - 4.90: 37637 Nonbonded interactions: 87398 Sorted by model distance: nonbonded pdb=" N2 DG X 12 " pdb=" O2 DC X 43 " model vdw 2.032 2.496 nonbonded pdb=" N GLU B 642 " pdb=" OE1 GLU B 642 " model vdw 2.078 2.520 nonbonded pdb=" CG2 VAL B 641 " pdb=" OE1 GLU B 642 " model vdw 2.113 3.460 nonbonded pdb=" CD1 LEU A 27 " pdb=" CA ALA A 281 " model vdw 2.202 3.890 nonbonded pdb=" OH TYR A 956 " pdb=" OP1 DT X 1 " model vdw 2.257 2.440 ... (remaining 87393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 35 5.49 5 S 40 5.16 5 C 7483 2.51 5 N 2210 2.21 5 O 2223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 5.480 Check model and map are aligned: 0.170 Process input model: 39.320 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.161 12268 Z= 0.570 Angle : 1.162 10.312 16911 Z= 0.649 Chirality : 0.063 0.495 2060 Planarity : 0.008 0.076 2053 Dihedral : 14.833 177.166 4191 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.14 % Favored : 89.79 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.00 (0.15), residues: 1518 helix: -4.70 (0.09), residues: 773 sheet: -2.49 (0.44), residues: 118 loop : -3.05 (0.20), residues: 627 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 239 time to evaluate : 1.170 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 248 average time/residue: 0.3484 time to fit residues: 112.0973 Evaluate side-chains 116 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 1.547 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1421 time to fit residues: 2.4188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9980 chunk 122 optimal weight: 0.2980 chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 0.0980 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 205 HIS B 229 GLN B 744 GLN A 496 HIS A 631 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 12268 Z= 0.181 Angle : 0.680 9.979 16911 Z= 0.347 Chirality : 0.042 0.268 2060 Planarity : 0.006 0.062 2053 Dihedral : 16.714 176.647 2004 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.17), residues: 1518 helix: -3.78 (0.12), residues: 769 sheet: -2.21 (0.48), residues: 108 loop : -2.65 (0.21), residues: 641 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.378 Fit side-chains outliers start: 29 outliers final: 10 residues processed: 159 average time/residue: 0.2547 time to fit residues: 58.9095 Evaluate side-chains 118 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.768 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1433 time to fit residues: 5.3220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 131 optimal weight: 0.0870 chunk 146 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 12268 Z= 0.213 Angle : 0.638 12.078 16911 Z= 0.322 Chirality : 0.042 0.224 2060 Planarity : 0.005 0.052 2053 Dihedral : 16.491 178.247 2004 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.19), residues: 1518 helix: -3.01 (0.15), residues: 766 sheet: -1.83 (0.52), residues: 104 loop : -2.23 (0.23), residues: 648 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 1.423 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 16 residues processed: 151 average time/residue: 0.2091 time to fit residues: 48.5858 Evaluate side-chains 123 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1106 time to fit residues: 5.0719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 744 GLN ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 643 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 12268 Z= 0.286 Angle : 0.667 13.107 16911 Z= 0.334 Chirality : 0.044 0.195 2060 Planarity : 0.005 0.063 2053 Dihedral : 16.493 179.116 2004 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.20), residues: 1518 helix: -2.60 (0.16), residues: 772 sheet: -1.64 (0.50), residues: 116 loop : -2.15 (0.24), residues: 630 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.382 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 133 average time/residue: 0.2135 time to fit residues: 44.1285 Evaluate side-chains 110 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.392 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1095 time to fit residues: 4.3374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 116 optimal weight: 0.0870 chunk 64 optimal weight: 3.9990 chunk 133 optimal weight: 0.0270 chunk 108 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 358 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 12268 Z= 0.307 Angle : 0.677 13.346 16911 Z= 0.340 Chirality : 0.045 0.220 2060 Planarity : 0.005 0.052 2053 Dihedral : 16.485 179.080 2004 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.20), residues: 1518 helix: -2.33 (0.17), residues: 778 sheet: -1.61 (0.49), residues: 116 loop : -2.15 (0.24), residues: 624 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.372 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 127 average time/residue: 0.2257 time to fit residues: 43.4015 Evaluate side-chains 107 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1114 time to fit residues: 4.1970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 12268 Z= 0.256 Angle : 0.643 12.540 16911 Z= 0.323 Chirality : 0.043 0.203 2060 Planarity : 0.004 0.045 2053 Dihedral : 16.387 179.234 2004 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.21), residues: 1518 helix: -2.02 (0.18), residues: 775 sheet: -1.53 (0.50), residues: 116 loop : -2.09 (0.24), residues: 627 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 117 average time/residue: 0.2200 time to fit residues: 40.0057 Evaluate side-chains 109 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.407 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1219 time to fit residues: 4.2625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 1.9990 chunk 17 optimal weight: 0.0370 chunk 89 optimal weight: 10.0000 chunk 114 optimal weight: 0.0050 chunk 88 optimal weight: 4.9990 chunk 131 optimal weight: 0.0980 chunk 87 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 95 optimal weight: 0.1980 chunk 72 optimal weight: 0.3980 overall best weight: 0.1472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 12268 Z= 0.139 Angle : 0.559 9.753 16911 Z= 0.285 Chirality : 0.039 0.188 2060 Planarity : 0.004 0.039 2053 Dihedral : 16.095 178.747 2004 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.21), residues: 1518 helix: -1.47 (0.19), residues: 757 sheet: -1.24 (0.52), residues: 117 loop : -1.96 (0.24), residues: 644 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.411 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 133 average time/residue: 0.2426 time to fit residues: 47.8683 Evaluate side-chains 109 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1226 time to fit residues: 2.2050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 142 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 12268 Z= 0.161 Angle : 0.574 10.402 16911 Z= 0.288 Chirality : 0.040 0.206 2060 Planarity : 0.004 0.040 2053 Dihedral : 15.894 178.339 2004 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.22), residues: 1518 helix: -1.19 (0.19), residues: 777 sheet: -1.16 (0.52), residues: 117 loop : -1.92 (0.24), residues: 624 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.213 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 120 average time/residue: 0.2066 time to fit residues: 38.9776 Evaluate side-chains 111 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1124 time to fit residues: 2.7013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 0.0980 chunk 114 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 0.0010 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 12268 Z= 0.140 Angle : 0.552 9.316 16911 Z= 0.277 Chirality : 0.040 0.208 2060 Planarity : 0.003 0.037 2053 Dihedral : 15.653 178.136 2004 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.22), residues: 1518 helix: -0.87 (0.20), residues: 765 sheet: -1.10 (0.52), residues: 117 loop : -1.76 (0.24), residues: 636 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 1.190 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 121 average time/residue: 0.2183 time to fit residues: 40.8459 Evaluate side-chains 111 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.312 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1320 time to fit residues: 2.3981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 0.0980 chunk 161 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 128 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 102 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 12268 Z= 0.164 Angle : 0.564 9.747 16911 Z= 0.282 Chirality : 0.040 0.216 2060 Planarity : 0.004 0.064 2053 Dihedral : 15.582 178.071 2004 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.22), residues: 1518 helix: -0.69 (0.20), residues: 772 sheet: -1.10 (0.52), residues: 117 loop : -1.73 (0.24), residues: 629 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 1.369 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 117 average time/residue: 0.2033 time to fit residues: 37.2761 Evaluate side-chains 110 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1089 time to fit residues: 2.3362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.145498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119944 restraints weight = 17415.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119724 restraints weight = 13851.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120291 restraints weight = 11826.943| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12268 Z= 0.223 Angle : 0.608 11.219 16911 Z= 0.305 Chirality : 0.042 0.209 2060 Planarity : 0.004 0.058 2053 Dihedral : 15.661 178.202 2004 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.22), residues: 1518 helix: -0.69 (0.20), residues: 770 sheet: -1.19 (0.52), residues: 117 loop : -1.75 (0.24), residues: 631 =============================================================================== Job complete usr+sys time: 2107.39 seconds wall clock time: 39 minutes 16.63 seconds (2356.63 seconds total)