Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 03:06:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yg8_10799/04_2023/6yg8_10799.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yg8_10799/04_2023/6yg8_10799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yg8_10799/04_2023/6yg8_10799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yg8_10799/04_2023/6yg8_10799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yg8_10799/04_2023/6yg8_10799.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yg8_10799/04_2023/6yg8_10799.pdb" } resolution = 3.0 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= 0.001 sd= 0.989 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 15442 2.51 5 N 4144 2.21 5 O 4629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 644": "OE1" <-> "OE2" Residue "A ARG 647": "NH1" <-> "NH2" Residue "A ARG 652": "NH1" <-> "NH2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B ARG 647": "NH1" <-> "NH2" Residue "B ARG 652": "NH1" <-> "NH2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 625": "OE1" <-> "OE2" Residue "C ARG 647": "NH1" <-> "NH2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C ARG 652": "NH1" <-> "NH2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D GLU 380": "OE1" <-> "OE2" Residue "D ARG 544": "NH1" <-> "NH2" Residue "D GLU 644": "OE1" <-> "OE2" Residue "D ARG 647": "NH1" <-> "NH2" Residue "D ARG 652": "NH1" <-> "NH2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 24330 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 4996 Classifications: {'peptide': 643} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 591} Chain breaks: 1 Chain: "B" Number of atoms: 4944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4944 Classifications: {'peptide': 637} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 585} Chain breaks: 2 Chain: "C" Number of atoms: 4944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4944 Classifications: {'peptide': 637} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 585} Chain breaks: 2 Chain: "D" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 4960 Classifications: {'peptide': 639} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 587} Chain breaks: 2 Chain: "E" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4486 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 529} Chain breaks: 4 Time building chain proxies: 11.76, per 1000 atoms: 0.48 Number of scatterers: 24330 At special positions: 0 Unit cell: (117.878, 135.77, 197.866, 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 115 16.00 O 4629 8.00 N 4144 7.00 C 15442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 500 " distance=2.03 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 500 " distance=2.03 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 500 " distance=2.03 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 500 " distance=2.03 Simple disulfide: pdb=" SG CYS E 182 " - pdb=" SG CYS E 500 " 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: 9.66 Conformation dependent library (CDL) restraints added in 3.5 seconds 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5834 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 55 sheets defined 19.0% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 145 through 149 removed outlier: 3.556A pdb=" N LEU A 149 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.876A pdb=" N ILE A 164 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 4.734A pdb=" N PHE A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 258 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 321 through 334 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 531 through 539 removed outlier: 3.533A pdb=" N PHE A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 560 through 579 Processing helix chain 'A' and resid 608 through 613 removed outlier: 4.057A pdb=" N ASP A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 696 Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.514A pdb=" N ALA A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 145 through 149 removed outlier: 3.624A pdb=" N LEU B 149 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 258 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 321 through 336 removed outlier: 3.730A pdb=" N ASN B 336 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 373 through 376 Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 531 through 539 removed outlier: 3.562A pdb=" N PHE B 535 " --> pdb=" O ASP B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 560 through 579 Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.833A pdb=" N THR B 593 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 594 " --> pdb=" O GLY B 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 590 through 594' Processing helix chain 'B' and resid 608 through 613 removed outlier: 4.039A pdb=" N ASP B 613 " --> pdb=" O ASP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 697 Processing helix chain 'B' and resid 697 through 702 Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 145 through 149 removed outlier: 3.508A pdb=" N GLN C 148 " --> pdb=" O THR C 145 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 149 " --> pdb=" O LYS C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 145 through 149' Processing helix chain 'C' and resid 212 through 215 Processing helix chain 'C' and resid 216 through 221 removed outlier: 4.746A pdb=" N PHE C 220 " --> pdb=" O PHE C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 258 Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 321 through 334 Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 378 through 381 removed outlier: 3.569A pdb=" N GLN C 381 " --> pdb=" O TYR C 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 378 through 381' Processing helix chain 'C' and resid 531 through 539 removed outlier: 3.740A pdb=" N PHE C 535 " --> pdb=" O ASP C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 544 Processing helix chain 'C' and resid 560 through 579 Processing helix chain 'C' and resid 608 through 613 removed outlier: 3.723A pdb=" N ASP C 613 " --> pdb=" O ASP C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 697 Processing helix chain 'C' and resid 697 through 702 Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.514A pdb=" N ALA D 81 " --> pdb=" O PHE D 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 77 through 81' Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 240 through 258 Processing helix chain 'D' and resid 321 through 334 removed outlier: 3.661A pdb=" N GLN D 327 " --> pdb=" O LYS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 531 through 538 removed outlier: 3.628A pdb=" N PHE D 535 " --> pdb=" O ASP D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 544 Processing helix chain 'D' and resid 562 through 579 Processing helix chain 'D' and resid 591 through 595 Processing helix chain 'D' and resid 608 through 613 removed outlier: 4.303A pdb=" N ASP D 613 " --> pdb=" O ASP D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 697 Processing helix chain 'D' and resid 697 through 702 Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 212 through 216 Processing helix chain 'E' and resid 240 through 258 Processing helix chain 'E' and resid 287 through 291 Processing helix chain 'E' and resid 321 through 334 removed outlier: 3.533A pdb=" N LEU E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 531 through 537 Processing helix chain 'E' and resid 539 through 544 Processing helix chain 'E' and resid 560 through 579 removed outlier: 3.635A pdb=" N THR E 566 " --> pdb=" O ALA E 562 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU E 567 " --> pdb=" O GLN E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 697 removed outlier: 3.790A pdb=" N GLU E 689 " --> pdb=" O PRO E 685 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET E 690 " --> pdb=" O ARG E 686 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU E 691 " --> pdb=" O GLY E 687 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP E 697 " --> pdb=" O ASP E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 697 through 702 removed outlier: 3.775A pdb=" N ARG E 701 " --> pdb=" O ASP E 697 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76 removed outlier: 6.510A pdb=" N GLY A 199 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU A 113 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP A 201 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA A 111 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A 203 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 76 removed outlier: 6.510A pdb=" N GLY A 199 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU A 113 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP A 201 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA A 111 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A 203 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA A 111 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 101 removed outlier: 6.294A pdb=" N LEU A 134 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 229 through 230 removed outlier: 6.315A pdb=" N ASN A 229 " --> pdb=" O ASN A 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 269 removed outlier: 6.698A pdb=" N VAL A 312 " --> pdb=" O HIS A 306 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL A 346 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR B 656 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR B 630 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG B 652 " --> pdb=" O VAL B 628 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B 628 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR B 654 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER B 626 " --> pdb=" O THR B 654 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 370 through 371 removed outlier: 4.472A pdb=" N ASP A 411 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 370 through 371 removed outlier: 4.472A pdb=" N ASP A 411 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 392 through 397 removed outlier: 3.684A pdb=" N GLN A 439 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU A 433 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N PHE A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 492 through 495 removed outlier: 6.319A pdb=" N CYS C 500 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 501 through 502 Processing sheet with id=AB2, first strand: chain 'A' and resid 526 through 529 Processing sheet with id=AB3, first strand: chain 'A' and resid 586 through 588 removed outlier: 6.558A pdb=" N THR A 551 " --> pdb=" O THR A 586 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR A 588 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR A 553 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 601 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU A 680 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE A 603 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA A 682 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG A 675 " --> pdb=" O SER A 669 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 619 through 621 removed outlier: 3.626A pdb=" N TRP A 627 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A 626 " --> pdb=" O THR A 654 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR A 654 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 628 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG A 652 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR A 630 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C 348 " --> pdb=" O THR A 654 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR A 656 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL C 346 " --> pdb=" O THR A 656 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA C 277 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL C 317 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 279 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 234 " --> pdb=" O PHE C 280 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N MET C 233 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 70 through 76 removed outlier: 6.574A pdb=" N GLY B 199 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU B 113 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP B 201 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA B 111 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR B 203 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 70 through 76 removed outlier: 6.574A pdb=" N GLY B 199 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU B 113 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP B 201 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA B 111 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR B 203 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 95 through 101 removed outlier: 6.407A pdb=" N LEU B 130 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL B 141 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 132 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 229 through 230 removed outlier: 6.188A pdb=" N ASN B 229 " --> pdb=" O ASN B 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 267 through 269 removed outlier: 6.697A pdb=" N ALA B 277 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL B 317 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 279 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLY B 319 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA B 281 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 312 " --> pdb=" O HIS B 306 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL B 346 " --> pdb=" O THR D 656 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR D 656 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU B 348 " --> pdb=" O THR D 654 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR D 654 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR D 630 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG D 652 " --> pdb=" O VAL D 628 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL D 628 " --> pdb=" O ARG D 652 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR D 654 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER D 626 " --> pdb=" O THR D 654 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP D 627 " --> pdb=" O LEU D 620 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 370 through 371 removed outlier: 3.998A pdb=" N ASP B 411 " --> pdb=" O ASP B 519 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN B 415 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 370 through 371 removed outlier: 3.998A pdb=" N ASP B 411 " --> pdb=" O ASP B 519 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 392 through 397 removed outlier: 6.571A pdb=" N MET B 429 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER B 440 " --> pdb=" O MET B 429 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 431 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 527 through 529 Processing sheet with id=AC5, first strand: chain 'B' and resid 586 through 588 removed outlier: 6.510A pdb=" N THR B 551 " --> pdb=" O THR B 586 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N THR B 588 " --> pdb=" O THR B 551 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N THR B 553 " --> pdb=" O THR B 588 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 70 through 76 removed outlier: 6.650A pdb=" N GLY C 199 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU C 113 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP C 201 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA C 111 " --> pdb=" O ASP C 201 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR C 203 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 70 through 76 removed outlier: 6.650A pdb=" N GLY C 199 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU C 113 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP C 201 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA C 111 " --> pdb=" O ASP C 201 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR C 203 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 95 through 101 removed outlier: 3.516A pdb=" N VAL C 170 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU C 130 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL C 141 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL C 132 " --> pdb=" O MET C 139 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 229 through 230 removed outlier: 6.127A pdb=" N ASN C 229 " --> pdb=" O ASN C 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 370 through 371 Processing sheet with id=AD2, first strand: chain 'C' and resid 370 through 371 Processing sheet with id=AD3, first strand: chain 'C' and resid 392 through 397 removed outlier: 6.412A pdb=" N MET C 429 " --> pdb=" O SER C 440 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER C 440 " --> pdb=" O MET C 429 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE C 431 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 492 through 493 Processing sheet with id=AD5, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AD6, first strand: chain 'C' and resid 586 through 588 removed outlier: 6.437A pdb=" N THR C 551 " --> pdb=" O THR C 586 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR C 588 " --> pdb=" O THR C 551 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR C 553 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE C 601 " --> pdb=" O ILE C 678 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU C 680 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE C 603 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ALA C 682 " --> pdb=" O ILE C 603 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 619 through 621 removed outlier: 6.581A pdb=" N SER C 626 " --> pdb=" O THR C 654 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR C 654 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL C 628 " --> pdb=" O ARG C 652 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG C 652 " --> pdb=" O VAL C 628 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C 630 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C 656 " --> pdb=" O VAL E 346 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL E 346 " --> pdb=" O THR C 656 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL E 312 " --> pdb=" O HIS E 306 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA E 277 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL E 317 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL E 279 " --> pdb=" O VAL E 317 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 70 through 76 removed outlier: 6.505A pdb=" N GLY D 199 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU D 113 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP D 201 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA D 111 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR D 203 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 70 through 76 removed outlier: 6.505A pdb=" N GLY D 199 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU D 113 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP D 201 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA D 111 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR D 203 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA D 111 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 95 through 101 removed outlier: 6.465A pdb=" N LEU D 130 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL D 141 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL D 132 " --> pdb=" O MET D 139 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 229 through 230 removed outlier: 6.304A pdb=" N ASN D 229 " --> pdb=" O ASN D 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 267 through 269 removed outlier: 5.764A pdb=" N VAL D 312 " --> pdb=" O HIS D 306 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 370 through 371 removed outlier: 3.581A pdb=" N ASP D 411 " --> pdb=" O ASP D 519 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 383 through 386 Processing sheet with id=AE6, first strand: chain 'D' and resid 392 through 397 removed outlier: 5.774A pdb=" N LEU D 433 " --> pdb=" O PHE D 437 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE D 437 " --> pdb=" O LEU D 433 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 402 through 403 Processing sheet with id=AE8, first strand: chain 'D' and resid 494 through 495 Processing sheet with id=AE9, first strand: chain 'D' and resid 527 through 528 Processing sheet with id=AF1, first strand: chain 'D' and resid 586 through 588 removed outlier: 6.338A pdb=" N THR D 551 " --> pdb=" O THR D 586 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR D 588 " --> pdb=" O THR D 551 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR D 553 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE D 552 " --> pdb=" O MET D 602 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE D 601 " --> pdb=" O ILE D 678 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU D 680 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE D 603 " --> pdb=" O LEU D 680 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ALA D 682 " --> pdb=" O ILE D 603 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 70 through 74 removed outlier: 6.835A pdb=" N ASP E 201 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA E 111 " --> pdb=" O ASP E 201 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR E 203 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 70 through 74 removed outlier: 6.835A pdb=" N ASP E 201 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA E 111 " --> pdb=" O ASP E 201 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR E 203 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 95 through 101 removed outlier: 6.448A pdb=" N LEU E 130 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL E 141 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL E 132 " --> pdb=" O MET E 139 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 229 through 230 removed outlier: 6.577A pdb=" N ASN E 229 " --> pdb=" O ASN E 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'E' and resid 369 through 371 Processing sheet with id=AF7, first strand: chain 'E' and resid 369 through 371 removed outlier: 4.758A pdb=" N ASN E 415 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASP E 515 " --> pdb=" O ASP E 413 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASP E 413 " --> pdb=" O ASP E 515 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR E 517 " --> pdb=" O ASP E 411 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP E 411 " --> pdb=" O THR E 517 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 392 through 397 removed outlier: 5.609A pdb=" N LEU E 433 " --> pdb=" O PHE E 437 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N PHE E 437 " --> pdb=" O LEU E 433 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 527 through 529 Processing sheet with id=AG1, first strand: chain 'E' and resid 586 through 588 removed outlier: 6.725A pdb=" N THR E 551 " --> pdb=" O THR E 586 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N THR E 588 " --> pdb=" O THR E 551 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR E 553 " --> pdb=" O THR E 588 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL E 554 " --> pdb=" O MET E 602 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE E 601 " --> pdb=" O ILE E 678 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU E 680 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE E 603 " --> pdb=" O LEU E 680 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ALA E 682 " --> pdb=" O ILE E 603 " (cutoff:3.500A) 876 hydrogen bonds defined for protein. 2343 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: 10.31 Time building geometry restraints manager: 10.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8122 1.34 - 1.46: 4823 1.46 - 1.58: 11723 1.58 - 1.69: 0 1.69 - 1.81: 220 Bond restraints: 24888 Sorted by residual: bond pdb=" C PRO A 491 " pdb=" N MET A 492 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.44e-02 4.82e+03 2.22e+00 bond pdb=" C LYS C 629 " pdb=" N THR C 630 " ideal model delta sigma weight residual 1.331 1.302 0.029 2.07e-02 2.33e+03 2.02e+00 bond pdb=" CA ALA C 473 " pdb=" C ALA C 473 " ideal model delta sigma weight residual 1.523 1.499 0.025 1.80e-02 3.09e+03 1.86e+00 bond pdb=" CA VAL D 724 " pdb=" CB VAL D 724 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.31e-02 5.83e+03 1.38e+00 bond pdb=" N ASP A 643 " pdb=" CA ASP A 643 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.27e+00 ... (remaining 24883 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.13: 813 105.13 - 112.35: 12446 112.35 - 119.57: 7826 119.57 - 126.79: 12438 126.79 - 134.01: 356 Bond angle restraints: 33879 Sorted by residual: angle pdb=" C ASN E 537 " pdb=" N ALA E 538 " pdb=" CA ALA E 538 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C LEU D 352 " pdb=" N LEU D 353 " pdb=" CA LEU D 353 " ideal model delta sigma weight residual 120.51 124.75 -4.24 1.45e+00 4.76e-01 8.54e+00 angle pdb=" N ASP D 515 " pdb=" CA ASP D 515 " pdb=" C ASP D 515 " ideal model delta sigma weight residual 113.28 108.80 4.48 1.57e+00 4.06e-01 8.15e+00 angle pdb=" C PRO C 273 " pdb=" N ASP C 274 " pdb=" CA ASP C 274 " ideal model delta sigma weight residual 122.61 126.90 -4.29 1.56e+00 4.11e-01 7.58e+00 angle pdb=" C ALA A 478 " pdb=" CA ALA A 478 " pdb=" CB ALA A 478 " ideal model delta sigma weight residual 110.42 115.70 -5.28 1.99e+00 2.53e-01 7.03e+00 ... (remaining 33874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 14040 17.51 - 35.02: 939 35.02 - 52.53: 131 52.53 - 70.04: 25 70.04 - 87.55: 13 Dihedral angle restraints: 15148 sinusoidal: 6108 harmonic: 9040 Sorted by residual: dihedral pdb=" CB CYS D 182 " pdb=" SG CYS D 182 " pdb=" SG CYS D 500 " pdb=" CB CYS D 500 " ideal model delta sinusoidal sigma weight residual 93.00 175.86 -82.86 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS B 182 " pdb=" SG CYS B 182 " pdb=" SG CYS B 500 " pdb=" CB CYS B 500 " ideal model delta sinusoidal sigma weight residual -86.00 -138.18 52.18 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CA HIS E 215 " pdb=" C HIS E 215 " pdb=" N PHE E 216 " pdb=" CA PHE E 216 " ideal model delta harmonic sigma weight residual -180.00 -150.79 -29.21 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 15145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2342 0.036 - 0.072: 947 0.072 - 0.108: 378 0.108 - 0.144: 119 0.144 - 0.180: 8 Chirality restraints: 3794 Sorted by residual: chirality pdb=" CB ILE E 80 " pdb=" CA ILE E 80 " pdb=" CG1 ILE E 80 " pdb=" CG2 ILE E 80 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA VAL D 218 " pdb=" N VAL D 218 " pdb=" C VAL D 218 " pdb=" CB VAL D 218 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CA PRO B 273 " pdb=" N PRO B 273 " pdb=" C PRO B 273 " pdb=" CB PRO B 273 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.24e-01 ... (remaining 3791 not shown) Planarity restraints: 4501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 82 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO E 83 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 83 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 83 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 124 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO C 125 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 218 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.86e+00 pdb=" N PRO D 219 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 219 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 219 " 0.024 5.00e-02 4.00e+02 ... (remaining 4498 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 984 2.71 - 3.26: 24121 3.26 - 3.81: 38697 3.81 - 4.35: 52071 4.35 - 4.90: 88697 Nonbonded interactions: 204570 Sorted by model distance: nonbonded pdb=" OD1 ASN A 347 " pdb=" OG1 THR B 656 " model vdw 2.166 2.440 nonbonded pdb=" NH2 ARG C 428 " pdb=" O GLN E 507 " model vdw 2.197 2.520 nonbonded pdb=" OH TYR D 418 " pdb=" O LEU D 443 " model vdw 2.202 2.440 nonbonded pdb=" OG SER B 122 " pdb=" OG1 THR B 189 " model vdw 2.209 2.440 nonbonded pdb=" OG SER C 122 " pdb=" OG1 THR C 189 " model vdw 2.213 2.440 ... (remaining 204565 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' and (resid 67 through 403 or resid 410 through 605 or resid 661 throu \ gh 710 or resid 717 through 728)) selection = (chain 'B' and (resid 67 through 403 or resid 410 through 443 or resid 465 throu \ gh 605 or resid 661 through 710 or resid 717 through 728)) selection = (chain 'C' and (resid 67 through 403 or resid 410 through 443 or resid 465 throu \ gh 605 or resid 661 through 710 or resid 717 through 728)) selection = (chain 'D' and (resid 67 through 403 or resid 410 through 443 or resid 465 throu \ gh 605 or resid 661 through 710 or resid 717 through 728)) selection = (chain 'E' and resid 67 through 728) } 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: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.410 Check model and map are aligned: 0.360 Set scattering table: 0.200 Process input model: 62.550 Find NCS groups from input model: 1.900 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: 0.010 Load rotamer database and sin/cos tables:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.005 0.043 24888 Z= 0.301 Angle : 0.602 7.642 33879 Z= 0.339 Chirality : 0.047 0.180 3794 Planarity : 0.004 0.050 4501 Dihedral : 11.985 87.554 9299 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -3.49 (0.13), residues: 3100 helix: -3.47 (0.15), residues: 422 sheet: -1.89 (0.15), residues: 909 loop : -2.27 (0.14), residues: 1769 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 3.112 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 1.3962 time to fit residues: 509.1623 Evaluate side-chains 224 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 130 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 696 ASN B 415 ASN C 79 GLN C 276 ASN C 435 ASN E 245 GLN E 334 GLN E 435 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 24888 Z= 0.227 Angle : 0.565 5.952 33879 Z= 0.291 Chirality : 0.047 0.167 3794 Planarity : 0.005 0.050 4501 Dihedral : 4.940 25.576 3358 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -2.24 (0.14), residues: 3100 helix: -1.23 (0.21), residues: 442 sheet: -1.25 (0.16), residues: 887 loop : -1.68 (0.14), residues: 1771 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 246 time to evaluate : 3.111 Fit side-chains outliers start: 53 outliers final: 18 residues processed: 270 average time/residue: 1.2556 time to fit residues: 397.2899 Evaluate side-chains 239 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 221 time to evaluate : 2.983 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 10 residues processed: 8 average time/residue: 0.4319 time to fit residues: 9.0959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 0.0970 chunk 87 optimal weight: 0.9990 chunk 234 optimal weight: 0.9990 chunk 191 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 282 optimal weight: 0.0970 chunk 304 optimal weight: 3.9990 chunk 251 optimal weight: 0.9980 chunk 279 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 215 HIS E 334 GLN E 383 GLN E 435 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 24888 Z= 0.189 Angle : 0.529 7.361 33879 Z= 0.270 Chirality : 0.046 0.165 3794 Planarity : 0.004 0.051 4501 Dihedral : 4.763 23.892 3358 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -1.55 (0.15), residues: 3100 helix: 0.02 (0.24), residues: 437 sheet: -0.95 (0.16), residues: 903 loop : -1.33 (0.15), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 232 time to evaluate : 3.081 Fit side-chains outliers start: 58 outliers final: 28 residues processed: 263 average time/residue: 1.2756 time to fit residues: 393.1864 Evaluate side-chains 239 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 time to evaluate : 3.057 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 19 residues processed: 9 average time/residue: 0.4009 time to fit residues: 9.5975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 283 optimal weight: 0.7980 chunk 299 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 268 optimal weight: 0.6980 chunk 80 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN E 334 GLN E 435 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 24888 Z= 0.196 Angle : 0.519 7.408 33879 Z= 0.265 Chirality : 0.046 0.255 3794 Planarity : 0.004 0.051 4501 Dihedral : 4.657 23.780 3358 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -1.11 (0.15), residues: 3100 helix: 0.59 (0.25), residues: 443 sheet: -0.68 (0.17), residues: 904 loop : -1.10 (0.15), residues: 1753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 236 time to evaluate : 2.947 Fit side-chains revert: symmetry clash outliers start: 66 outliers final: 36 residues processed: 276 average time/residue: 1.2465 time to fit residues: 406.7098 Evaluate side-chains 252 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 216 time to evaluate : 2.918 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 27 residues processed: 9 average time/residue: 0.5283 time to fit residues: 10.4062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 255 optimal weight: 0.0000 chunk 207 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN E 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 24888 Z= 0.264 Angle : 0.536 7.724 33879 Z= 0.273 Chirality : 0.047 0.215 3794 Planarity : 0.004 0.051 4501 Dihedral : 4.704 23.873 3358 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -0.93 (0.15), residues: 3100 helix: 0.72 (0.25), residues: 443 sheet: -0.54 (0.17), residues: 914 loop : -0.99 (0.15), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 228 time to evaluate : 3.030 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 43 residues processed: 274 average time/residue: 1.1854 time to fit residues: 383.7296 Evaluate side-chains 263 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 220 time to evaluate : 2.864 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 31 residues processed: 12 average time/residue: 0.4658 time to fit residues: 11.8028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 2.9990 chunk 269 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 299 optimal weight: 2.9990 chunk 248 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 99 optimal weight: 0.0070 chunk 157 optimal weight: 3.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 160 ASN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 24888 Z= 0.199 Angle : 0.521 7.640 33879 Z= 0.265 Chirality : 0.046 0.192 3794 Planarity : 0.004 0.051 4501 Dihedral : 4.635 23.505 3358 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3100 helix: 0.92 (0.25), residues: 443 sheet: -0.37 (0.17), residues: 925 loop : -0.86 (0.15), residues: 1732 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 227 time to evaluate : 2.903 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 43 residues processed: 272 average time/residue: 1.1818 time to fit residues: 382.7617 Evaluate side-chains 270 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 227 time to evaluate : 2.864 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 32 residues processed: 12 average time/residue: 0.6236 time to fit residues: 13.6335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 252 optimal weight: 0.1980 chunk 167 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 chunk 186 optimal weight: 0.0370 chunk 182 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 507 GLN B 499 ASN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN E 499 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 24888 Z= 0.198 Angle : 0.517 7.138 33879 Z= 0.263 Chirality : 0.046 0.179 3794 Planarity : 0.004 0.054 4501 Dihedral : 4.571 23.236 3358 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -0.53 (0.15), residues: 3100 helix: 1.06 (0.25), residues: 443 sheet: -0.22 (0.17), residues: 933 loop : -0.77 (0.15), residues: 1724 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 239 time to evaluate : 2.824 Fit side-chains revert: symmetry clash outliers start: 66 outliers final: 38 residues processed: 281 average time/residue: 1.1954 time to fit residues: 395.8585 Evaluate side-chains 258 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 220 time to evaluate : 2.986 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 30 residues processed: 8 average time/residue: 0.3167 time to fit residues: 8.1748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 2.9990 chunk 119 optimal weight: 0.0570 chunk 178 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 24888 Z= 0.292 Angle : 0.551 9.222 33879 Z= 0.278 Chirality : 0.047 0.172 3794 Planarity : 0.004 0.051 4501 Dihedral : 4.696 23.411 3358 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -0.50 (0.15), residues: 3100 helix: 0.96 (0.25), residues: 443 sheet: -0.19 (0.17), residues: 932 loop : -0.72 (0.15), residues: 1725 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 221 time to evaluate : 2.953 Fit side-chains revert: symmetry clash outliers start: 62 outliers final: 38 residues processed: 261 average time/residue: 1.2794 time to fit residues: 396.8110 Evaluate side-chains 257 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 219 time to evaluate : 2.949 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 31 residues processed: 8 average time/residue: 0.5675 time to fit residues: 10.4312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 278 optimal weight: 1.9990 chunk 167 optimal weight: 0.0870 chunk 121 optimal weight: 0.6980 chunk 218 optimal weight: 6.9990 chunk 85 optimal weight: 0.4980 chunk 251 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN E 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 24888 Z= 0.236 Angle : 0.533 9.502 33879 Z= 0.270 Chirality : 0.047 0.174 3794 Planarity : 0.004 0.052 4501 Dihedral : 4.656 23.359 3358 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -0.38 (0.15), residues: 3100 helix: 1.04 (0.25), residues: 449 sheet: -0.12 (0.17), residues: 931 loop : -0.63 (0.15), residues: 1720 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 226 time to evaluate : 3.087 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 36 residues processed: 264 average time/residue: 1.1906 time to fit residues: 372.4480 Evaluate side-chains 256 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 220 time to evaluate : 3.099 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 5 average time/residue: 0.5705 time to fit residues: 7.9988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 308 optimal weight: 8.9990 chunk 284 optimal weight: 0.9990 chunk 245 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 150 optimal weight: 0.3980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 24888 Z= 0.200 Angle : 0.537 10.418 33879 Z= 0.271 Chirality : 0.046 0.198 3794 Planarity : 0.004 0.054 4501 Dihedral : 4.675 33.064 3358 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.30 (0.15), residues: 3100 helix: 1.15 (0.25), residues: 449 sheet: -0.08 (0.17), residues: 935 loop : -0.58 (0.16), residues: 1716 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 222 time to evaluate : 3.102 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 35 residues processed: 259 average time/residue: 1.2534 time to fit residues: 384.3310 Evaluate side-chains 255 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 220 time to evaluate : 2.875 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 33 residues processed: 3 average time/residue: 0.3450 time to fit residues: 5.5977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 226 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN E 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.107640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.085151 restraints weight = 41821.754| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.25 r_work: 0.3017 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 24888 Z= 0.278 Angle : 0.554 9.992 33879 Z= 0.279 Chirality : 0.047 0.182 3794 Planarity : 0.004 0.053 4501 Dihedral : 4.731 29.275 3358 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -0.38 (0.15), residues: 3100 helix: 1.05 (0.25), residues: 449 sheet: -0.14 (0.17), residues: 943 loop : -0.62 (0.16), residues: 1708 =============================================================================== Job complete usr+sys time: 7405.60 seconds wall clock time: 133 minutes 6.72 seconds (7986.72 seconds total)