Starting phenix.real_space_refine on Tue Apr 9 21:07:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl3_25190/04_2024/7sl3_25190_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl3_25190/04_2024/7sl3_25190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl3_25190/04_2024/7sl3_25190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl3_25190/04_2024/7sl3_25190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl3_25190/04_2024/7sl3_25190_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl3_25190/04_2024/7sl3_25190_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3460 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 8898 2.51 5 N 2408 2.21 5 O 2598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "F GLU 4": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14016 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6629 Classifications: {'peptide': 820} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 774} Chain breaks: 6 Chain: "B" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6629 Classifications: {'peptide': 820} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 774} Chain breaks: 6 Chain: "C" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "D" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "E" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "F" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Time building chain proxies: 8.17, per 1000 atoms: 0.58 Number of scatterers: 14016 At special positions: 0 Unit cell: (139.32, 115.56, 174.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 2598 8.00 N 2408 7.00 C 8898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.04 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS E 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS E 20 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS F 20 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 11 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.27 Conformation dependent library (CDL) restraints added in 2.5 seconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 34 sheets defined 17.2% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.977A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 24 " --> pdb=" O HIS A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 24' Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.733A pdb=" N PHE A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.817A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.593A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.801A pdb=" N GLU A 318 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.695A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.521A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.502A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.962A pdb=" N PHE A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 640 through 645' Processing helix chain 'A' and resid 691 through 716 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 18 through 24 removed outlier: 4.066A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 24 " --> pdb=" O HIS B 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 18 through 24' Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.719A pdb=" N PHE B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.837A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.584A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.807A pdb=" N GLU B 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.686A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.511A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.506A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 640 through 645 removed outlier: 4.028A pdb=" N PHE B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 640 through 645' Processing helix chain 'B' and resid 690 through 716 removed outlier: 5.283A pdb=" N LYS B 696 " --> pdb=" O SER B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.768A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 19 removed outlier: 3.745A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 13 through 20 removed outlier: 3.536A pdb=" N GLU E 17 " --> pdb=" O TYR E 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 13 through 20 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 3.502A pdb=" N LEU A 36 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS A 121 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.844A pdb=" N VAL A 179 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA9, first strand: chain 'A' and resid 319 through 321 removed outlier: 3.550A pdb=" N LEU A 368 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N HIS A 429 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A 403 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.772A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.619A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 601 through 607 removed outlier: 5.897A pdb=" N ASP A 602 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS A 618 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 613 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 770 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 636 through 637 removed outlier: 4.045A pdb=" N GLY A 780 " --> pdb=" O GLN A 637 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 630 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL A 632 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 762 " --> pdb=" O VAL A 632 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 636 through 637 removed outlier: 4.045A pdb=" N GLY A 780 " --> pdb=" O GLN A 637 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 821 through 824 removed outlier: 3.553A pdb=" N VAL A 830 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 858 through 864 removed outlier: 6.896A pdb=" N THR A 891 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR A 847 " --> pdb=" O ARG A 889 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG A 889 " --> pdb=" O TYR A 847 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 849 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG A 887 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR A 851 " --> pdb=" O SER A 885 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER A 885 " --> pdb=" O TYR A 851 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG A 853 " --> pdb=" O ASN A 883 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASN A 883 " --> pdb=" O ARG A 853 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 882 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.598A pdb=" N LEU B 36 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 121 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.840A pdb=" N VAL B 179 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.580A pdb=" N HIS B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.718A pdb=" N PHE B 231 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC6, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AC7, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC9, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.543A pdb=" N LEU B 368 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE B 427 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR B 401 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N HIS B 429 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU B 403 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD2, first strand: chain 'B' and resid 475 through 480 removed outlier: 6.735A pdb=" N ARG B 488 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE B 478 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 486 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.548A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 601 through 606 removed outlier: 5.599A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 761 through 764 removed outlier: 3.509A pdb=" N GLU B 762 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL B 632 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AD7, first strand: chain 'B' and resid 858 through 864 removed outlier: 6.847A pdb=" N THR B 891 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR B 847 " --> pdb=" O ARG B 889 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG B 889 " --> pdb=" O TYR B 847 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 849 " --> pdb=" O ARG B 887 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG B 887 " --> pdb=" O VAL B 849 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR B 851 " --> pdb=" O SER B 885 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER B 885 " --> pdb=" O TYR B 851 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG B 853 " --> pdb=" O ASN B 883 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASN B 883 " --> pdb=" O ARG B 853 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY B 882 " --> pdb=" O VAL B 907 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.95 Time building geometry restraints manager: 5.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4591 1.34 - 1.46: 3333 1.46 - 1.58: 6298 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 14358 Sorted by residual: bond pdb=" CA THR B 690 " pdb=" CB THR B 690 " ideal model delta sigma weight residual 1.518 1.540 -0.023 2.08e-02 2.31e+03 1.18e+00 bond pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.13e+00 bond pdb=" CA LYS B 559 " pdb=" CB LYS B 559 " ideal model delta sigma weight residual 1.519 1.537 -0.017 1.73e-02 3.34e+03 9.81e-01 bond pdb=" CA CYS B 687 " pdb=" C CYS B 687 " ideal model delta sigma weight residual 1.524 1.516 0.008 8.10e-03 1.52e+04 9.47e-01 bond pdb=" CA LYS A 559 " pdb=" CB LYS A 559 " ideal model delta sigma weight residual 1.519 1.536 -0.016 1.73e-02 3.34e+03 9.03e-01 ... (remaining 14353 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.51: 463 106.51 - 113.39: 7606 113.39 - 120.26: 5005 120.26 - 127.13: 6197 127.13 - 134.00: 189 Bond angle restraints: 19460 Sorted by residual: angle pdb=" C THR B 580 " pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 121.54 132.53 -10.99 1.91e+00 2.74e-01 3.31e+01 angle pdb=" C THR A 580 " pdb=" N TYR A 581 " pdb=" CA TYR A 581 " ideal model delta sigma weight residual 121.54 131.73 -10.19 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C THR B 690 " pdb=" CA THR B 690 " pdb=" CB THR B 690 " ideal model delta sigma weight residual 115.79 109.56 6.23 1.19e+00 7.06e-01 2.74e+01 angle pdb=" N ASP A 691 " pdb=" CA ASP A 691 " pdb=" C ASP A 691 " ideal model delta sigma weight residual 113.41 109.26 4.15 1.22e+00 6.72e-01 1.16e+01 angle pdb=" N SER B 692 " pdb=" CA SER B 692 " pdb=" C SER B 692 " ideal model delta sigma weight residual 113.19 109.62 3.57 1.19e+00 7.06e-01 8.98e+00 ... (remaining 19455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7931 17.94 - 35.87: 628 35.87 - 53.81: 114 53.81 - 71.74: 29 71.74 - 89.68: 10 Dihedral angle restraints: 8712 sinusoidal: 3640 harmonic: 5072 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 155 " pdb=" CB CYS B 155 " ideal model delta sinusoidal sigma weight residual -86.00 -148.27 62.27 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual -86.00 -147.43 61.43 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 147.12 -54.12 1 1.00e+01 1.00e-02 3.97e+01 ... (remaining 8709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1357 0.034 - 0.068: 490 0.068 - 0.101: 164 0.101 - 0.135: 95 0.135 - 0.169: 4 Chirality restraints: 2110 Sorted by residual: chirality pdb=" CB THR B 690 " pdb=" CA THR B 690 " pdb=" OG1 THR B 690 " pdb=" CG2 THR B 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB THR A 690 " pdb=" CA THR A 690 " pdb=" OG1 THR A 690 " pdb=" CG2 THR A 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 2107 not shown) Planarity restraints: 2516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 580 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C THR B 580 " -0.042 2.00e-02 2.50e+03 pdb=" O THR B 580 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR B 581 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 580 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C THR A 580 " -0.039 2.00e-02 2.50e+03 pdb=" O THR A 580 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 581 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 836 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A 837 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 837 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 837 " 0.017 5.00e-02 4.00e+02 ... (remaining 2513 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2332 2.77 - 3.30: 13128 3.30 - 3.84: 22468 3.84 - 4.37: 26556 4.37 - 4.90: 45564 Nonbonded interactions: 110048 Sorted by model distance: nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.238 2.440 nonbonded pdb=" NH2 ARG A 14 " pdb=" O VAL B 715 " model vdw 2.241 2.520 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.244 2.440 nonbonded pdb=" O VAL A 715 " pdb=" NH2 ARG B 14 " model vdw 2.245 2.520 nonbonded pdb=" NE2 GLN A 790 " pdb=" O ASP A 794 " model vdw 2.246 2.520 ... (remaining 110043 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 7.670 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 38.750 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.002 0.039 14358 Z= 0.160 Angle : 0.537 10.991 19460 Z= 0.287 Chirality : 0.043 0.169 2110 Planarity : 0.003 0.031 2516 Dihedral : 13.247 89.680 5316 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.35 % Favored : 93.41 % Rotamer: Outliers : 0.32 % Allowed : 0.32 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.71 (0.21), residues: 1700 helix: -0.32 (0.36), residues: 222 sheet: 0.84 (0.30), residues: 334 loop : -0.95 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 412 HIS 0.003 0.000 HIS A 440 PHE 0.013 0.001 PHE B 778 TYR 0.014 0.001 TYR B 581 ARG 0.003 0.000 ARG B 578 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 1.620 Fit side-chains revert: symmetry clash REVERT: B 687 CYS cc_start: 0.2703 (OUTLIER) cc_final: 0.2494 (m) REVERT: F 17 GLU cc_start: 0.7541 (mp0) cc_final: 0.7209 (mp0) outliers start: 5 outliers final: 2 residues processed: 72 average time/residue: 0.2488 time to fit residues: 28.5198 Evaluate side-chains 55 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 689 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 44 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 134 optimal weight: 0.5980 chunk 52 optimal weight: 0.2980 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 30.0000 chunk 156 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14358 Z= 0.190 Angle : 0.515 6.446 19460 Z= 0.272 Chirality : 0.044 0.193 2110 Planarity : 0.003 0.031 2516 Dihedral : 4.826 54.082 1905 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.18 % Favored : 93.71 % Rotamer: Outliers : 0.25 % Allowed : 4.05 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.53 (0.21), residues: 1700 helix: 0.46 (0.38), residues: 210 sheet: 0.87 (0.30), residues: 324 loop : -0.91 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 412 HIS 0.003 0.001 HIS B 831 PHE 0.011 0.001 PHE A 567 TYR 0.012 0.001 TYR B 507 ARG 0.005 0.000 ARG A 782 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 1.748 Fit side-chains REVERT: A 175 ASN cc_start: 0.6752 (p0) cc_final: 0.6380 (p0) REVERT: B 175 ASN cc_start: 0.6713 (p0) cc_final: 0.6360 (p0) REVERT: F 17 GLU cc_start: 0.7790 (mp0) cc_final: 0.7549 (mp0) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 0.2528 time to fit residues: 26.4880 Evaluate side-chains 51 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 156 optimal weight: 0.6980 chunk 169 optimal weight: 0.0980 chunk 139 optimal weight: 6.9990 chunk 155 optimal weight: 0.0370 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14358 Z= 0.158 Angle : 0.488 6.347 19460 Z= 0.256 Chirality : 0.043 0.184 2110 Planarity : 0.003 0.034 2516 Dihedral : 4.452 35.062 1900 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.00 % Favored : 93.88 % Rotamer: Outliers : 0.13 % Allowed : 7.02 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.49 (0.21), residues: 1700 helix: 0.62 (0.38), residues: 210 sheet: 0.64 (0.30), residues: 334 loop : -0.84 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 412 HIS 0.002 0.001 HIS B 831 PHE 0.012 0.001 PHE B 707 TYR 0.018 0.001 TYR B 581 ARG 0.004 0.000 ARG A 782 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ASN cc_start: 0.6727 (p0) cc_final: 0.6433 (p0) REVERT: A 833 MET cc_start: 0.5190 (mmt) cc_final: 0.4518 (tpt) REVERT: B 175 ASN cc_start: 0.6730 (p0) cc_final: 0.6427 (p0) REVERT: F 17 GLU cc_start: 0.7735 (mp0) cc_final: 0.7391 (mp0) outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 0.2412 time to fit residues: 23.0291 Evaluate side-chains 50 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 17 optimal weight: 0.0770 chunk 74 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 166 optimal weight: 0.0050 chunk 82 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14358 Z= 0.163 Angle : 0.481 7.892 19460 Z= 0.253 Chirality : 0.043 0.184 2110 Planarity : 0.003 0.032 2516 Dihedral : 4.466 35.156 1900 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.94 % Favored : 93.94 % Rotamer: Outliers : 0.32 % Allowed : 8.60 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1700 helix: 0.74 (0.38), residues: 208 sheet: 0.65 (0.30), residues: 334 loop : -0.86 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 412 HIS 0.003 0.001 HIS A 440 PHE 0.011 0.001 PHE A 567 TYR 0.020 0.001 TYR B 581 ARG 0.002 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ASN cc_start: 0.6759 (p0) cc_final: 0.6308 (p0) REVERT: A 442 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8197 (ttp) REVERT: A 833 MET cc_start: 0.5178 (mmt) cc_final: 0.4469 (tpt) REVERT: B 38 MET cc_start: 0.8044 (tpp) cc_final: 0.7358 (mtp) REVERT: B 174 ILE cc_start: 0.8898 (tp) cc_final: 0.8675 (tt) REVERT: B 175 ASN cc_start: 0.6786 (p0) cc_final: 0.6322 (p0) REVERT: E 17 GLU cc_start: 0.7236 (mp0) cc_final: 0.6800 (mp0) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 0.2362 time to fit residues: 25.1625 Evaluate side-chains 57 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 141 optimal weight: 0.0980 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 149 optimal weight: 0.0570 chunk 41 optimal weight: 1.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 452 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14358 Z= 0.189 Angle : 0.484 7.150 19460 Z= 0.254 Chirality : 0.043 0.182 2110 Planarity : 0.003 0.034 2516 Dihedral : 4.481 34.388 1900 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.06 % Favored : 93.82 % Rotamer: Outliers : 0.44 % Allowed : 10.30 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1700 helix: 0.78 (0.38), residues: 208 sheet: 0.68 (0.30), residues: 344 loop : -0.89 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 412 HIS 0.003 0.001 HIS A 440 PHE 0.011 0.001 PHE A 567 TYR 0.022 0.001 TYR B 581 ARG 0.003 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.7853 (ppp) cc_final: 0.7651 (ptt) REVERT: A 98 MET cc_start: 0.8933 (mmm) cc_final: 0.8490 (tpt) REVERT: A 175 ASN cc_start: 0.6803 (p0) cc_final: 0.6369 (p0) REVERT: A 442 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8163 (ttp) REVERT: A 833 MET cc_start: 0.5511 (mmt) cc_final: 0.4864 (tpt) REVERT: B 38 MET cc_start: 0.8067 (tpp) cc_final: 0.7410 (mtp) REVERT: B 174 ILE cc_start: 0.8867 (tp) cc_final: 0.8662 (tt) REVERT: B 175 ASN cc_start: 0.6855 (p0) cc_final: 0.6366 (p0) REVERT: E 17 GLU cc_start: 0.7480 (mp0) cc_final: 0.7075 (mp0) outliers start: 7 outliers final: 2 residues processed: 61 average time/residue: 0.2218 time to fit residues: 22.5470 Evaluate side-chains 54 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 32 optimal weight: 0.0570 chunk 97 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 138 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14358 Z= 0.152 Angle : 0.473 8.221 19460 Z= 0.247 Chirality : 0.042 0.182 2110 Planarity : 0.003 0.031 2516 Dihedral : 4.366 35.012 1900 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.82 % Favored : 94.06 % Rotamer: Outliers : 0.57 % Allowed : 11.19 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.46 (0.21), residues: 1700 helix: 0.79 (0.38), residues: 208 sheet: 0.68 (0.30), residues: 334 loop : -0.86 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 412 HIS 0.002 0.000 HIS B 440 PHE 0.011 0.001 PHE B 707 TYR 0.022 0.001 TYR B 581 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.7861 (ppp) cc_final: 0.7650 (ptm) REVERT: A 98 MET cc_start: 0.8938 (mmm) cc_final: 0.8436 (tpt) REVERT: A 175 ASN cc_start: 0.6829 (p0) cc_final: 0.6368 (p0) REVERT: A 442 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8180 (ttp) REVERT: A 833 MET cc_start: 0.5505 (mmt) cc_final: 0.4863 (tpt) REVERT: B 38 MET cc_start: 0.8024 (tpp) cc_final: 0.7376 (mtt) REVERT: B 175 ASN cc_start: 0.6864 (p0) cc_final: 0.6361 (p0) REVERT: B 782 ARG cc_start: 0.9109 (mmm-85) cc_final: 0.8745 (mmm-85) REVERT: E 17 GLU cc_start: 0.7495 (mp0) cc_final: 0.7142 (mp0) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.2518 time to fit residues: 25.1822 Evaluate side-chains 59 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 92 optimal weight: 0.0980 chunk 165 optimal weight: 0.8980 chunk 103 optimal weight: 0.0060 chunk 101 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 66 optimal weight: 0.0980 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14358 Z= 0.194 Angle : 0.489 8.911 19460 Z= 0.253 Chirality : 0.043 0.180 2110 Planarity : 0.003 0.032 2516 Dihedral : 4.374 34.197 1900 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.12 % Favored : 93.76 % Rotamer: Outliers : 0.70 % Allowed : 11.69 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1700 helix: 0.81 (0.38), residues: 208 sheet: 0.74 (0.30), residues: 344 loop : -0.88 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 412 HIS 0.004 0.001 HIS B 440 PHE 0.011 0.001 PHE A 567 TYR 0.024 0.001 TYR B 581 ARG 0.002 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.688 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.8981 (mmm) cc_final: 0.8498 (tpt) REVERT: A 110 MET cc_start: 0.8143 (mmm) cc_final: 0.7933 (mtp) REVERT: A 175 ASN cc_start: 0.6824 (p0) cc_final: 0.6369 (p0) REVERT: A 442 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8258 (ttp) REVERT: A 833 MET cc_start: 0.5513 (mmt) cc_final: 0.4867 (tpt) REVERT: B 38 MET cc_start: 0.8060 (tpp) cc_final: 0.7411 (mtt) REVERT: B 175 ASN cc_start: 0.6889 (p0) cc_final: 0.6425 (p0) REVERT: B 782 ARG cc_start: 0.9123 (mmm-85) cc_final: 0.8734 (mmm-85) REVERT: E 17 GLU cc_start: 0.7511 (mp0) cc_final: 0.7176 (mp0) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.2358 time to fit residues: 24.3029 Evaluate side-chains 61 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 144 optimal weight: 0.1980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14358 Z= 0.193 Angle : 0.486 6.494 19460 Z= 0.253 Chirality : 0.042 0.179 2110 Planarity : 0.003 0.033 2516 Dihedral : 4.404 34.374 1900 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.12 % Favored : 93.76 % Rotamer: Outliers : 0.70 % Allowed : 12.14 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.51 (0.21), residues: 1700 helix: 0.78 (0.38), residues: 208 sheet: 0.54 (0.30), residues: 354 loop : -0.88 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 553 HIS 0.004 0.001 HIS A 440 PHE 0.020 0.001 PHE A 778 TYR 0.023 0.001 TYR B 581 ARG 0.002 0.000 ARG C 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 1.622 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.8947 (mmm) cc_final: 0.8463 (tpt) REVERT: A 110 MET cc_start: 0.8137 (mmm) cc_final: 0.7923 (mtp) REVERT: A 833 MET cc_start: 0.5289 (mmt) cc_final: 0.4728 (tpt) REVERT: B 38 MET cc_start: 0.8024 (tpp) cc_final: 0.7249 (mtt) REVERT: B 782 ARG cc_start: 0.9114 (mmm-85) cc_final: 0.8732 (mmm-85) REVERT: E 17 GLU cc_start: 0.7492 (mp0) cc_final: 0.7164 (mp0) outliers start: 11 outliers final: 9 residues processed: 62 average time/residue: 0.2776 time to fit residues: 27.6235 Evaluate side-chains 61 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 92 optimal weight: 0.0050 chunk 67 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14358 Z= 0.226 Angle : 0.508 8.718 19460 Z= 0.265 Chirality : 0.043 0.178 2110 Planarity : 0.003 0.035 2516 Dihedral : 4.497 33.804 1900 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.24 % Favored : 93.65 % Rotamer: Outliers : 0.76 % Allowed : 12.45 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.57 (0.21), residues: 1700 helix: 0.71 (0.37), residues: 208 sheet: 0.40 (0.29), residues: 360 loop : -0.88 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 412 HIS 0.005 0.001 HIS A 440 PHE 0.014 0.001 PHE A 778 TYR 0.024 0.001 TYR B 581 ARG 0.003 0.000 ARG A 806 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 1.695 Fit side-chains revert: symmetry clash REVERT: A 442 MET cc_start: 0.8740 (ttm) cc_final: 0.8140 (tpp) REVERT: A 833 MET cc_start: 0.5341 (mmt) cc_final: 0.4821 (tpt) REVERT: B 38 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7285 (mtt) REVERT: B 782 ARG cc_start: 0.9110 (mmm-85) cc_final: 0.8814 (mmm-85) REVERT: E 17 GLU cc_start: 0.7559 (mp0) cc_final: 0.7215 (mp0) outliers start: 12 outliers final: 8 residues processed: 62 average time/residue: 0.2440 time to fit residues: 24.7482 Evaluate side-chains 63 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14358 Z= 0.358 Angle : 0.585 6.617 19460 Z= 0.305 Chirality : 0.045 0.178 2110 Planarity : 0.004 0.037 2516 Dihedral : 4.882 35.724 1900 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.41 % Favored : 92.53 % Rotamer: Outliers : 0.63 % Allowed : 12.64 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.78 (0.21), residues: 1700 helix: 0.46 (0.37), residues: 218 sheet: 0.12 (0.29), residues: 364 loop : -0.97 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 183 HIS 0.006 0.001 HIS A 440 PHE 0.017 0.002 PHE A 778 TYR 0.030 0.002 TYR B 581 ARG 0.003 0.001 ARG A 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 1.691 Fit side-chains revert: symmetry clash REVERT: A 442 MET cc_start: 0.8909 (ttm) cc_final: 0.8141 (tpp) REVERT: B 38 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7360 (mtt) REVERT: E 14 TYR cc_start: 0.7835 (t80) cc_final: 0.7289 (t80) REVERT: E 17 GLU cc_start: 0.7514 (mp0) cc_final: 0.7190 (mp0) outliers start: 10 outliers final: 7 residues processed: 57 average time/residue: 0.2389 time to fit residues: 22.7120 Evaluate side-chains 60 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 136 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.103385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.070151 restraints weight = 40337.913| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.35 r_work: 0.3119 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14358 Z= 0.157 Angle : 0.510 7.200 19460 Z= 0.266 Chirality : 0.043 0.175 2110 Planarity : 0.003 0.038 2516 Dihedral : 4.621 34.426 1900 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.82 % Favored : 94.12 % Rotamer: Outliers : 0.57 % Allowed : 12.77 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.65 (0.21), residues: 1700 helix: 0.60 (0.37), residues: 208 sheet: 0.29 (0.29), residues: 360 loop : -0.91 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 412 HIS 0.003 0.001 HIS A 440 PHE 0.015 0.001 PHE A 778 TYR 0.016 0.001 TYR B 512 ARG 0.004 0.000 ARG A 806 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2719.72 seconds wall clock time: 50 minutes 57.65 seconds (3057.65 seconds total)