Starting phenix.real_space_refine on Tue Mar 19 14:05:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yg8_10799/03_2024/6yg8_10799.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yg8_10799/03_2024/6yg8_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_10799/03_2024/6yg8_10799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yg8_10799/03_2024/6yg8_10799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yg8_10799/03_2024/6yg8_10799.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yg8_10799/03_2024/6yg8_10799.pdb" } resolution = 3.0 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= 0.001 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.01, per 1000 atoms: 0.49 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: 8.37 Conformation dependent library (CDL) restraints added in 3.8 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: 3.22 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: 9.94 Time building geometry restraints manager: 9.14 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: 3.820 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: 0.030 Extract box with map and model: 16.560 Check model and map are aligned: 0.400 Set scattering table: 0.230 Process input model: 61.350 Find NCS groups from input model: 1.910 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:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.320 ------------------------------------------------------------------------------- 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 % Allowed : 2.43 % Favored : 97.57 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 627 HIS 0.005 0.001 HIS A 306 PHE 0.016 0.002 PHE A 667 TYR 0.013 0.001 TYR A 523 ARG 0.003 0.000 ARG A 365 *********************** 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 : 3.101 Fit side-chains revert: symmetry clash REVERT: B 359 ASP cc_start: 0.8204 (t0) cc_final: 0.7775 (t0) REVERT: B 415 ASN cc_start: 0.7765 (m-40) cc_final: 0.7296 (m110) REVERT: D 74 LYS cc_start: 0.8109 (tptp) cc_final: 0.7904 (tmtt) REVERT: D 87 MET cc_start: 0.8705 (ptp) cc_final: 0.8264 (ptp) REVERT: D 403 TYR cc_start: 0.6827 (t80) cc_final: 0.6423 (t80) REVERT: D 435 ASN cc_start: 0.8658 (t0) cc_final: 0.7985 (t0) REVERT: E 412 MET cc_start: 0.8404 (ptt) cc_final: 0.8201 (ptt) REVERT: E 602 MET cc_start: 0.8555 (ttm) cc_final: 0.8086 (ttp) REVERT: E 725 TYR cc_start: 0.6375 (m-80) cc_final: 0.5990 (m-10) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 1.3710 time to fit residues: 498.4249 Evaluate side-chains 228 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.505 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24888 Z= 0.227 Angle : 0.563 5.923 33879 Z= 0.289 Chirality : 0.047 0.165 3794 Planarity : 0.005 0.050 4501 Dihedral : 4.947 24.504 3358 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.92 % Allowed : 8.26 % Favored : 89.82 % 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: -2.28 (0.14), residues: 3100 helix: -1.29 (0.21), residues: 442 sheet: -1.28 (0.16), residues: 887 loop : -1.69 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 253 HIS 0.004 0.001 HIS C 306 PHE 0.022 0.002 PHE D 573 TYR 0.014 0.001 TYR C 523 ARG 0.009 0.000 ARG E 169 *********************** 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 296 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 244 time to evaluate : 2.829 Fit side-chains REVERT: A 387 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8467 (mm) REVERT: A 420 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.8024 (tpt) REVERT: A 523 TYR cc_start: 0.7221 (m-80) cc_final: 0.6944 (m-10) REVERT: B 359 ASP cc_start: 0.8213 (t0) cc_final: 0.7902 (t0) REVERT: C 318 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8513 (m-80) REVERT: C 704 MET cc_start: 0.8905 (mtm) cc_final: 0.8650 (mtt) REVERT: D 215 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.7001 (p90) REVERT: D 303 MET cc_start: 0.8679 (ttt) cc_final: 0.8474 (ttt) REVERT: D 403 TYR cc_start: 0.6696 (t80) cc_final: 0.6245 (t80) REVERT: D 435 ASN cc_start: 0.8656 (t0) cc_final: 0.7967 (t0) REVERT: D 704 MET cc_start: 0.8496 (mtt) cc_final: 0.8177 (mtm) REVERT: D 713 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8412 (mm-30) REVERT: E 481 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7521 (mm-40) REVERT: E 602 MET cc_start: 0.8487 (ttm) cc_final: 0.8022 (ttp) REVERT: E 725 TYR cc_start: 0.6222 (m-80) cc_final: 0.5889 (m-10) outliers start: 52 outliers final: 19 residues processed: 269 average time/residue: 1.2046 time to fit residues: 378.9379 Evaluate side-chains 251 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 226 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 723 ASP Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 664 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 234 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 282 optimal weight: 0.3980 chunk 304 optimal weight: 0.6980 chunk 251 optimal weight: 0.9990 chunk 279 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN E 93 ASN E 215 HIS E 334 GLN E 383 GLN E 435 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24888 Z= 0.223 Angle : 0.536 7.314 33879 Z= 0.274 Chirality : 0.047 0.162 3794 Planarity : 0.004 0.050 4501 Dihedral : 4.797 23.732 3358 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.36 % Allowed : 9.96 % Favored : 87.68 % 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: -0.06 (0.24), residues: 437 sheet: -0.95 (0.16), residues: 902 loop : -1.31 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 253 HIS 0.005 0.001 HIS C 215 PHE 0.023 0.001 PHE E 441 TYR 0.017 0.001 TYR C 523 ARG 0.010 0.000 ARG A 368 *********************** 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 302 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 238 time to evaluate : 2.902 Fit side-chains REVERT: A 420 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.8007 (tpt) REVERT: A 523 TYR cc_start: 0.7321 (m-80) cc_final: 0.6824 (m-10) REVERT: B 359 ASP cc_start: 0.8230 (t0) cc_final: 0.7894 (t0) REVERT: B 499 ASN cc_start: 0.8343 (t0) cc_final: 0.8128 (t0) REVERT: D 112 MET cc_start: 0.8175 (tpp) cc_final: 0.7816 (mmt) REVERT: D 169 ARG cc_start: 0.7688 (mtm110) cc_final: 0.7116 (tpp80) REVERT: D 215 HIS cc_start: 0.7463 (OUTLIER) cc_final: 0.6986 (p90) REVERT: D 403 TYR cc_start: 0.6653 (t80) cc_final: 0.6310 (t80) REVERT: D 411 ASP cc_start: 0.7997 (t0) cc_final: 0.7564 (p0) REVERT: D 435 ASN cc_start: 0.8664 (t0) cc_final: 0.7989 (t0) REVERT: D 704 MET cc_start: 0.8502 (mtt) cc_final: 0.8199 (mtm) REVERT: E 116 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: E 380 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7054 (mm-30) REVERT: E 481 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7533 (mm-40) REVERT: E 602 MET cc_start: 0.8456 (ttm) cc_final: 0.7998 (ttp) REVERT: E 725 TYR cc_start: 0.6180 (m-80) cc_final: 0.5859 (m-10) outliers start: 64 outliers final: 30 residues processed: 272 average time/residue: 1.1859 time to fit residues: 378.3767 Evaluate side-chains 253 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 219 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 215 HIS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 723 ASP Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 481 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 0.6980 chunk 212 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 283 optimal weight: 0.9980 chunk 299 optimal weight: 0.0980 chunk 147 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 80 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 334 GLN E 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24888 Z= 0.217 Angle : 0.524 7.303 33879 Z= 0.266 Chirality : 0.047 0.258 3794 Planarity : 0.004 0.050 4501 Dihedral : 4.707 23.807 3358 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.77 % Allowed : 11.18 % Favored : 86.06 % 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: -1.15 (0.15), residues: 3100 helix: 0.50 (0.24), residues: 443 sheet: -0.72 (0.17), residues: 904 loop : -1.10 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 253 HIS 0.005 0.001 HIS C 215 PHE 0.019 0.001 PHE D 573 TYR 0.018 0.001 TYR C 523 ARG 0.005 0.000 ARG A 368 *********************** 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 318 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 243 time to evaluate : 2.807 Fit side-chains revert: symmetry clash REVERT: A 420 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7972 (tpt) REVERT: A 523 TYR cc_start: 0.7192 (m-80) cc_final: 0.6932 (m-10) REVERT: B 359 ASP cc_start: 0.8233 (t0) cc_final: 0.7692 (t0) REVERT: B 499 ASN cc_start: 0.8336 (t0) cc_final: 0.8074 (t0) REVERT: B 661 MET cc_start: 0.8841 (ttp) cc_final: 0.8573 (ttp) REVERT: C 704 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8546 (mtm) REVERT: D 112 MET cc_start: 0.8154 (tpp) cc_final: 0.7730 (mmt) REVERT: D 169 ARG cc_start: 0.7671 (mtm110) cc_final: 0.7097 (tpp80) REVERT: D 215 HIS cc_start: 0.7559 (OUTLIER) cc_final: 0.7091 (p90) REVERT: D 403 TYR cc_start: 0.6646 (t80) cc_final: 0.6368 (t80) REVERT: D 411 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7464 (p0) REVERT: D 420 MET cc_start: 0.8200 (ttm) cc_final: 0.7894 (ttp) REVERT: D 435 ASN cc_start: 0.8670 (t0) cc_final: 0.7980 (t0) REVERT: D 704 MET cc_start: 0.8563 (mtt) cc_final: 0.8309 (mtm) REVERT: E 116 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: E 439 GLN cc_start: 0.7174 (tt0) cc_final: 0.6936 (tt0) REVERT: E 481 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7565 (mm-40) REVERT: E 602 MET cc_start: 0.8463 (ttm) cc_final: 0.8023 (ttp) REVERT: E 603 ILE cc_start: 0.9227 (pt) cc_final: 0.9007 (pp) REVERT: E 725 TYR cc_start: 0.6319 (m-80) cc_final: 0.5984 (m-10) outliers start: 75 outliers final: 41 residues processed: 283 average time/residue: 1.1819 time to fit residues: 392.2806 Evaluate side-chains 272 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 225 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 723 ASP Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 664 VAL 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: 0.7980 chunk 4 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 255 optimal weight: 0.6980 chunk 207 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN A 507 GLN E 334 GLN E 435 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24888 Z= 0.279 Angle : 0.542 7.877 33879 Z= 0.275 Chirality : 0.047 0.207 3794 Planarity : 0.004 0.050 4501 Dihedral : 4.750 24.120 3358 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.69 % Allowed : 12.84 % Favored : 84.47 % 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: -0.94 (0.15), residues: 3100 helix: 0.69 (0.25), residues: 437 sheet: -0.56 (0.17), residues: 917 loop : -0.98 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 253 HIS 0.006 0.001 HIS C 306 PHE 0.020 0.002 PHE D 573 TYR 0.019 0.001 TYR C 523 ARG 0.007 0.000 ARG C 291 *********************** 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 304 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 231 time to evaluate : 2.810 Fit side-chains revert: symmetry clash REVERT: A 420 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7988 (tpt) REVERT: A 523 TYR cc_start: 0.7278 (m-80) cc_final: 0.7049 (m-10) REVERT: B 359 ASP cc_start: 0.8229 (t0) cc_final: 0.7651 (t0) REVERT: B 499 ASN cc_start: 0.8309 (t0) cc_final: 0.7897 (m110) REVERT: B 661 MET cc_start: 0.8779 (ttp) cc_final: 0.8420 (ttp) REVERT: C 573 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8213 (p90) REVERT: C 633 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.7788 (ttm-80) REVERT: C 704 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8620 (mtt) REVERT: D 112 MET cc_start: 0.8119 (tpp) cc_final: 0.7775 (mmt) REVERT: D 215 HIS cc_start: 0.7586 (OUTLIER) cc_final: 0.7152 (p90) REVERT: D 411 ASP cc_start: 0.7964 (t0) cc_final: 0.7466 (p0) REVERT: D 435 ASN cc_start: 0.8673 (t0) cc_final: 0.7981 (t0) REVERT: D 704 MET cc_start: 0.8615 (mtt) cc_final: 0.8314 (mtm) REVERT: E 116 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: E 439 GLN cc_start: 0.7400 (tt0) cc_final: 0.7130 (tt0) REVERT: E 481 GLN cc_start: 0.7909 (tt0) cc_final: 0.7584 (mm-40) REVERT: E 602 MET cc_start: 0.8464 (ttm) cc_final: 0.8020 (ttp) REVERT: E 603 ILE cc_start: 0.9231 (pt) cc_final: 0.9024 (pp) REVERT: E 725 TYR cc_start: 0.6287 (m-80) cc_final: 0.6050 (m-10) outliers start: 73 outliers final: 40 residues processed: 273 average time/residue: 1.1643 time to fit residues: 373.5574 Evaluate side-chains 269 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 224 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 215 HIS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 723 ASP Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 664 VAL 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: 0.9980 chunk 59 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 442 ASN E 334 GLN E 435 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1647 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= 0.254 Angle : 0.530 6.726 33879 Z= 0.269 Chirality : 0.047 0.194 3794 Planarity : 0.004 0.051 4501 Dihedral : 4.728 24.093 3358 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.80 % Allowed : 13.24 % Favored : 83.95 % 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: -0.78 (0.15), residues: 3100 helix: 0.81 (0.25), residues: 437 sheet: -0.41 (0.17), residues: 926 loop : -0.90 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 253 HIS 0.005 0.001 HIS C 215 PHE 0.019 0.001 PHE D 573 TYR 0.016 0.001 TYR C 523 ARG 0.007 0.000 ARG C 291 *********************** 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 302 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 226 time to evaluate : 2.912 Fit side-chains revert: symmetry clash REVERT: A 420 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7984 (tpt) REVERT: A 523 TYR cc_start: 0.7231 (m-80) cc_final: 0.6965 (m-10) REVERT: B 359 ASP cc_start: 0.8229 (t0) cc_final: 0.7653 (t0) REVERT: B 499 ASN cc_start: 0.8308 (t0) cc_final: 0.7899 (m110) REVERT: B 661 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8575 (ttp) REVERT: C 573 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8186 (p90) REVERT: C 704 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8544 (mtm) REVERT: D 112 MET cc_start: 0.8138 (tpp) cc_final: 0.7778 (mmt) REVERT: D 215 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.7175 (p90) REVERT: D 411 ASP cc_start: 0.7923 (t0) cc_final: 0.7445 (p0) REVERT: D 435 ASN cc_start: 0.8661 (t0) cc_final: 0.7970 (t0) REVERT: D 638 PRO cc_start: 0.7833 (Cg_endo) cc_final: 0.7540 (Cg_exo) REVERT: D 704 MET cc_start: 0.8613 (mtt) cc_final: 0.8328 (mtm) REVERT: E 481 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7580 (mm-40) REVERT: E 602 MET cc_start: 0.8463 (ttm) cc_final: 0.8011 (ttp) REVERT: E 725 TYR cc_start: 0.6262 (m-80) cc_final: 0.6046 (m-10) outliers start: 76 outliers final: 45 residues processed: 269 average time/residue: 1.1862 time to fit residues: 375.1230 Evaluate side-chains 276 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 225 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 215 HIS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 723 ASP Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 664 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 0.1980 chunk 33 optimal weight: 0.4980 chunk 170 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 298 optimal weight: 0.0980 chunk 186 optimal weight: 0.9980 chunk 182 optimal weight: 0.0870 chunk 137 optimal weight: 1.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN E 160 ASN E 435 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24888 Z= 0.153 Angle : 0.505 7.066 33879 Z= 0.255 Chirality : 0.046 0.186 3794 Planarity : 0.004 0.051 4501 Dihedral : 4.545 23.126 3358 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.43 % Allowed : 13.83 % Favored : 83.73 % 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: -0.53 (0.15), residues: 3100 helix: 1.05 (0.25), residues: 449 sheet: -0.23 (0.17), residues: 936 loop : -0.76 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 253 HIS 0.004 0.001 HIS C 215 PHE 0.018 0.001 PHE E 441 TYR 0.013 0.001 TYR D 403 ARG 0.007 0.000 ARG C 291 *********************** 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 312 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 246 time to evaluate : 2.641 Fit side-chains revert: symmetry clash REVERT: A 523 TYR cc_start: 0.7153 (m-80) cc_final: 0.6934 (m-10) REVERT: B 359 ASP cc_start: 0.8193 (t0) cc_final: 0.7830 (t0) REVERT: B 499 ASN cc_start: 0.8270 (t0) cc_final: 0.7999 (t0) REVERT: B 661 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8580 (ttp) REVERT: C 573 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8061 (p90) REVERT: C 633 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.8129 (ptp-170) REVERT: D 112 MET cc_start: 0.8125 (tpp) cc_final: 0.7748 (mmt) REVERT: D 215 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.7108 (p90) REVERT: D 411 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7396 (p0) REVERT: D 435 ASN cc_start: 0.8652 (t0) cc_final: 0.7931 (t0) REVERT: D 638 PRO cc_start: 0.7891 (Cg_endo) cc_final: 0.7623 (Cg_exo) REVERT: D 704 MET cc_start: 0.8584 (mtt) cc_final: 0.8313 (mtm) REVERT: E 116 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7008 (tm-30) REVERT: E 481 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7628 (mm-40) REVERT: E 485 ASP cc_start: 0.7087 (t0) cc_final: 0.6874 (t0) REVERT: E 602 MET cc_start: 0.8485 (ttm) cc_final: 0.7974 (ttp) outliers start: 66 outliers final: 35 residues processed: 282 average time/residue: 1.2269 time to fit residues: 407.2555 Evaluate side-chains 265 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 224 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 723 ASP Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 664 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 1.9990 chunk 119 optimal weight: 0.0980 chunk 178 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 147 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24888 Z= 0.229 Angle : 0.526 8.863 33879 Z= 0.265 Chirality : 0.046 0.175 3794 Planarity : 0.004 0.052 4501 Dihedral : 4.578 23.360 3358 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.36 % Allowed : 14.42 % Favored : 83.22 % 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: -0.44 (0.15), residues: 3100 helix: 1.05 (0.25), residues: 449 sheet: -0.15 (0.17), residues: 944 loop : -0.70 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 253 HIS 0.005 0.001 HIS C 215 PHE 0.017 0.001 PHE D 573 TYR 0.014 0.001 TYR E 725 ARG 0.008 0.000 ARG C 291 *********************** 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 295 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 231 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7957 (tpt) REVERT: A 523 TYR cc_start: 0.7187 (m-80) cc_final: 0.6959 (m-10) REVERT: B 359 ASP cc_start: 0.8219 (t0) cc_final: 0.7641 (t0) REVERT: B 499 ASN cc_start: 0.8276 (t0) cc_final: 0.8021 (t0) REVERT: B 661 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8498 (ttp) REVERT: C 573 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8166 (p90) REVERT: C 633 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.8100 (ptp-170) REVERT: D 112 MET cc_start: 0.8127 (tpp) cc_final: 0.7747 (mmt) REVERT: D 215 HIS cc_start: 0.7508 (OUTLIER) cc_final: 0.7127 (p90) REVERT: D 411 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7385 (p0) REVERT: D 435 ASN cc_start: 0.8682 (t0) cc_final: 0.7951 (t0) REVERT: D 492 MET cc_start: 0.8549 (mtm) cc_final: 0.7721 (mtm) REVERT: D 638 PRO cc_start: 0.7921 (Cg_endo) cc_final: 0.7656 (Cg_exo) REVERT: D 704 MET cc_start: 0.8623 (mtt) cc_final: 0.8354 (mtm) REVERT: E 116 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: E 481 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7641 (mm-40) REVERT: E 485 ASP cc_start: 0.7202 (t0) cc_final: 0.6983 (t0) REVERT: E 602 MET cc_start: 0.8511 (ttm) cc_final: 0.7978 (ttp) outliers start: 64 outliers final: 39 residues processed: 270 average time/residue: 1.1594 time to fit residues: 368.5195 Evaluate side-chains 272 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 226 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 723 ASP Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 664 VAL 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: 0.6980 chunk 261 optimal weight: 0.1980 chunk 278 optimal weight: 3.9990 chunk 167 optimal weight: 0.0060 chunk 121 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 251 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 chunk 277 optimal weight: 0.0010 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24888 Z= 0.155 Angle : 0.510 8.964 33879 Z= 0.257 Chirality : 0.045 0.177 3794 Planarity : 0.004 0.053 4501 Dihedral : 4.467 22.743 3358 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.07 % Allowed : 14.94 % Favored : 83.00 % 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: -0.27 (0.15), residues: 3100 helix: 1.22 (0.25), residues: 461 sheet: -0.05 (0.17), residues: 930 loop : -0.61 (0.16), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 253 HIS 0.004 0.001 HIS C 215 PHE 0.016 0.001 PHE B 573 TYR 0.019 0.001 TYR E 725 ARG 0.008 0.000 ARG E 291 *********************** 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 306 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 250 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 TYR cc_start: 0.7135 (m-80) cc_final: 0.6898 (m-10) REVERT: B 350 LYS cc_start: 0.8951 (tttt) cc_final: 0.8700 (ttpt) REVERT: B 359 ASP cc_start: 0.8186 (t0) cc_final: 0.7914 (t0) REVERT: B 499 ASN cc_start: 0.8280 (t0) cc_final: 0.8010 (t0) REVERT: B 661 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8632 (ttp) REVERT: C 573 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.7969 (p90) REVERT: C 704 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8467 (mtm) REVERT: D 112 MET cc_start: 0.8103 (tpp) cc_final: 0.7712 (mmt) REVERT: D 215 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.7148 (p90) REVERT: D 252 SER cc_start: 0.8779 (t) cc_final: 0.8472 (p) REVERT: D 420 MET cc_start: 0.8122 (ttm) cc_final: 0.7815 (ttp) REVERT: D 435 ASN cc_start: 0.8658 (t0) cc_final: 0.7970 (t0) REVERT: D 638 PRO cc_start: 0.7920 (Cg_endo) cc_final: 0.7676 (Cg_exo) REVERT: D 704 MET cc_start: 0.8614 (mtt) cc_final: 0.8352 (mtm) REVERT: E 116 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: E 481 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7632 (mm-40) REVERT: E 485 ASP cc_start: 0.7071 (t0) cc_final: 0.6865 (t0) REVERT: E 602 MET cc_start: 0.8480 (ttm) cc_final: 0.8032 (ttp) outliers start: 56 outliers final: 37 residues processed: 281 average time/residue: 1.2523 time to fit residues: 414.2184 Evaluate side-chains 272 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 229 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 573 PHE Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 723 ASP Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 308 optimal weight: 7.9990 chunk 284 optimal weight: 0.0980 chunk 245 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 150 optimal weight: 0.0070 overall best weight: 1.6204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN E 435 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 24888 Z= 0.393 Angle : 0.596 9.400 33879 Z= 0.300 Chirality : 0.049 0.195 3794 Planarity : 0.005 0.053 4501 Dihedral : 4.826 29.268 3358 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.77 % Allowed : 15.64 % Favored : 82.59 % 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: -0.46 (0.15), residues: 3100 helix: 0.91 (0.25), residues: 443 sheet: -0.18 (0.17), residues: 941 loop : -0.66 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 253 HIS 0.008 0.002 HIS A 306 PHE 0.021 0.002 PHE D 573 TYR 0.014 0.001 TYR E 204 ARG 0.010 0.000 ARG C 291 ********************** 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 277 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 229 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ARG cc_start: 0.8443 (ttm110) cc_final: 0.8175 (ptt90) REVERT: A 523 TYR cc_start: 0.7251 (m-80) cc_final: 0.6983 (m-10) REVERT: B 350 LYS cc_start: 0.8987 (tttt) cc_final: 0.8701 (ttpt) REVERT: B 359 ASP cc_start: 0.8240 (t0) cc_final: 0.7806 (t0) REVERT: B 499 ASN cc_start: 0.8305 (t0) cc_final: 0.8052 (t0) REVERT: B 661 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8564 (ttp) REVERT: C 573 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8201 (p90) REVERT: C 646 ASP cc_start: 0.7207 (m-30) cc_final: 0.6957 (m-30) REVERT: C 704 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8589 (mtm) REVERT: D 112 MET cc_start: 0.8154 (tpp) cc_final: 0.7781 (mmt) REVERT: D 215 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.7171 (p90) REVERT: D 403 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.6377 (t80) REVERT: D 420 MET cc_start: 0.8103 (ttm) cc_final: 0.7829 (ttp) REVERT: D 435 ASN cc_start: 0.8678 (t0) cc_final: 0.7987 (t0) REVERT: D 638 PRO cc_start: 0.7953 (Cg_endo) cc_final: 0.7685 (Cg_exo) REVERT: D 661 MET cc_start: 0.8746 (ttp) cc_final: 0.8516 (ttp) REVERT: D 704 MET cc_start: 0.8641 (mtt) cc_final: 0.8333 (mtm) REVERT: E 116 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: E 481 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7624 (mm-40) REVERT: E 485 ASP cc_start: 0.7256 (t0) cc_final: 0.7021 (t0) REVERT: E 602 MET cc_start: 0.8562 (ttm) cc_final: 0.8081 (ttp) REVERT: E 690 MET cc_start: 0.8349 (mpt) cc_final: 0.7909 (pmm) outliers start: 48 outliers final: 33 residues processed: 261 average time/residue: 1.2470 time to fit residues: 380.0175 Evaluate side-chains 263 residues out of total 2711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 223 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 403 TYR Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 723 ASP Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 226 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 252 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.108193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.085704 restraints weight = 41568.175| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.25 r_work: 0.3031 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 : 0.003 0.043 24888 Z= 0.217 Angle : 0.544 9.785 33879 Z= 0.273 Chirality : 0.046 0.171 3794 Planarity : 0.004 0.054 4501 Dihedral : 4.710 26.890 3358 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.99 % Allowed : 15.57 % Favored : 82.44 % 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: -0.32 (0.15), residues: 3100 helix: 1.09 (0.25), residues: 449 sheet: -0.10 (0.17), residues: 933 loop : -0.58 (0.16), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 253 HIS 0.005 0.001 HIS C 215 PHE 0.016 0.001 PHE B 573 TYR 0.012 0.001 TYR D 403 ARG 0.009 0.000 ARG C 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7195.51 seconds wall clock time: 128 minutes 46.81 seconds (7726.81 seconds total)