Starting phenix.real_space_refine on Thu Mar 5 18:09:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yg8_10799/03_2026/6yg8_10799.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yg8_10799/03_2026/6yg8_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/cci-nas-00/data/ceres_data/6yg8_10799/03_2026/6yg8_10799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yg8_10799/03_2026/6yg8_10799.map" model { file = "/net/cci-nas-00/data/ceres_data/6yg8_10799/03_2026/6yg8_10799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yg8_10799/03_2026/6yg8_10799.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 5.43, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 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: 2.03 Conformation dependent library (CDL) restraints added in 984.3 milliseconds 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: 0.97 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: 4.71 Time building geometry restraints manager: 2.66 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: 0.00 - 1.53: 32927 1.53 - 3.06: 816 3.06 - 4.58: 112 4.58 - 6.11: 21 6.11 - 7.64: 3 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 3.040 nonbonded pdb=" NH2 ARG C 428 " pdb=" O GLN E 507 " model vdw 2.197 3.120 nonbonded pdb=" OH TYR D 418 " pdb=" O LEU D 443 " model vdw 2.202 3.040 nonbonded pdb=" OG SER B 122 " pdb=" OG1 THR B 189 " model vdw 2.209 3.040 nonbonded pdb=" OG SER C 122 " pdb=" OG1 THR C 189 " model vdw 2.213 3.040 ... (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 Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 67 through 403 or resid 410 through 605 or resid 661 throu \ gh 710 or resid 717 through 728)) selection = (chain 'B' and (resid 67 through 403 or resid 410 through 443 or resid 465 throu \ gh 605 or resid 661 through 710 or resid 717 through 728)) selection = (chain 'C' and (resid 67 through 403 or resid 410 through 443 or resid 465 throu \ gh 605 or resid 661 through 710 or resid 717 through 728)) selection = (chain 'D' and (resid 67 through 403 or resid 410 through 443 or resid 465 throu \ gh 605 or resid 661 through 710 or resid 717 through 728)) selection = (chain 'E' and resid 67 through 728) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 21.880 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.450 ------------------------------------------------------------------------------- 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 24893 Z= 0.204 Angle : 0.603 7.642 33889 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG A 365 TYR 0.013 0.001 TYR A 523 PHE 0.016 0.002 PHE A 667 TRP 0.010 0.001 TRP D 627 HIS 0.005 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00460 (24888) covalent geometry : angle 0.60231 (33879) SS BOND : bond 0.00156 ( 5) SS BOND : angle 1.50463 ( 10) hydrogen bonds : bond 0.21880 ( 817) hydrogen bonds : angle 10.27222 ( 2343) *********************** 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 to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 519 ASP cc_start: 0.8330 (t0) cc_final: 0.8083 (t0) REVERT: A 523 TYR cc_start: 0.7309 (m-80) cc_final: 0.6907 (m-10) 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: 0.7325 (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: 0.6424 (t80) REVERT: D 435 ASN cc_start: 0.8658 (t0) cc_final: 0.7984 (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: 0.5989 (m-10) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.6682 time to fit residues: 242.1162 Evaluate side-chains 228 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN C 276 ASN C 435 ASN E 245 GLN E 435 ASN E 537 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.103607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.081192 restraints weight = 41772.443| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.24 r_work: 0.2963 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 24893 Z= 0.245 Angle : 0.622 6.178 33889 Z= 0.322 Chirality : 0.049 0.174 3794 Planarity : 0.005 0.050 4501 Dihedral : 5.163 26.668 3358 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.10 % Allowed : 8.15 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.14), residues: 3100 helix: -1.39 (0.21), residues: 453 sheet: -1.33 (0.16), residues: 905 loop : -1.71 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 291 TYR 0.016 0.001 TYR C 523 PHE 0.024 0.002 PHE D 573 TRP 0.013 0.001 TRP A 253 HIS 0.007 0.002 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00577 (24888) covalent geometry : angle 0.62194 (33879) SS BOND : bond 0.01353 ( 5) SS BOND : angle 1.16442 ( 10) hydrogen bonds : bond 0.04377 ( 817) hydrogen bonds : angle 6.63856 ( 2343) *********************** 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 308 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 251 time to evaluate : 1.002 Fit side-chains REVERT: A 291 ARG cc_start: 0.8579 (ttp-110) cc_final: 0.8330 (ptp90) REVERT: A 368 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8341 (ttm170) REVERT: A 387 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8494 (mm) REVERT: A 420 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8626 (tpt) REVERT: A 492 MET cc_start: 0.8248 (mtm) cc_final: 0.7989 (ptp) REVERT: A 523 TYR cc_start: 0.7744 (m-80) cc_final: 0.7396 (m-10) REVERT: B 359 ASP cc_start: 0.8849 (t0) cc_final: 0.8311 (t0) REVERT: C 633 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.8084 (ttm-80) REVERT: C 704 MET cc_start: 0.9092 (mtm) cc_final: 0.8837 (mtt) REVERT: D 215 HIS cc_start: 0.7519 (OUTLIER) cc_final: 0.7087 (p90) REVERT: D 359 ASP cc_start: 0.8376 (t0) cc_final: 0.7923 (t0) REVERT: D 403 TYR cc_start: 0.6957 (t80) cc_final: 0.6445 (t80) REVERT: D 435 ASN cc_start: 0.8988 (t0) cc_final: 0.8365 (t0) REVERT: D 515 ASP cc_start: 0.7980 (m-30) cc_final: 0.7689 (m-30) REVERT: D 644 GLU cc_start: 0.7221 (mt-10) cc_final: 0.5872 (tp30) REVERT: E 334 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8504 (mm110) REVERT: E 481 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7895 (mm-40) REVERT: E 602 MET cc_start: 0.8749 (ttm) cc_final: 0.8299 (ttp) REVERT: E 725 TYR cc_start: 0.6492 (m-80) cc_final: 0.6077 (m-10) outliers start: 57 outliers final: 17 residues processed: 281 average time/residue: 0.5846 time to fit residues: 190.4379 Evaluate side-chains 249 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 153 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 282 THR 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 501 ILE Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 724 VAL 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 106 optimal weight: 0.9990 chunk 230 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 94 optimal weight: 0.4980 chunk 199 optimal weight: 0.9990 chunk 308 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 GLN B 415 ASN E 215 HIS E 383 GLN E 435 ASN E 537 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.105489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.083405 restraints weight = 41611.778| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.20 r_work: 0.3040 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24893 Z= 0.160 Angle : 0.554 7.052 33889 Z= 0.285 Chirality : 0.047 0.163 3794 Planarity : 0.005 0.049 4501 Dihedral : 4.940 26.118 3358 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.32 % Allowed : 9.96 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.15), residues: 3100 helix: -0.17 (0.24), residues: 449 sheet: -1.04 (0.16), residues: 900 loop : -1.33 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 533 TYR 0.018 0.001 TYR C 523 PHE 0.023 0.002 PHE E 441 TRP 0.012 0.001 TRP A 253 HIS 0.005 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00372 (24888) covalent geometry : angle 0.55362 (33879) SS BOND : bond 0.00323 ( 5) SS BOND : angle 1.48167 ( 10) hydrogen bonds : bond 0.03603 ( 817) hydrogen bonds : angle 5.95696 ( 2343) *********************** 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 307 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 244 time to evaluate : 0.798 Fit side-chains REVERT: A 368 ARG cc_start: 0.8552 (ttp80) cc_final: 0.8304 (ttm170) REVERT: A 415 ASN cc_start: 0.8269 (m-40) cc_final: 0.7850 (m110) REVERT: A 420 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8591 (tpt) REVERT: A 466 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8092 (ttmm) REVERT: A 523 TYR cc_start: 0.7723 (m-80) cc_final: 0.7273 (m-80) REVERT: B 359 ASP cc_start: 0.8818 (t0) cc_final: 0.8273 (t0) REVERT: B 499 ASN cc_start: 0.8456 (t0) cc_final: 0.7977 (m110) REVERT: B 598 ASP cc_start: 0.8139 (t0) cc_final: 0.7882 (t0) REVERT: D 112 MET cc_start: 0.8572 (tpp) cc_final: 0.8277 (mmt) REVERT: D 146 LYS cc_start: 0.9241 (tppt) cc_final: 0.8938 (mptt) REVERT: D 215 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.7023 (p90) REVERT: D 359 ASP cc_start: 0.8357 (t0) cc_final: 0.7879 (t0) REVERT: D 403 TYR cc_start: 0.6918 (t80) cc_final: 0.6520 (t80) REVERT: D 411 ASP cc_start: 0.8430 (t0) cc_final: 0.7720 (p0) REVERT: D 435 ASN cc_start: 0.8946 (t0) cc_final: 0.8348 (t0) REVERT: D 544 ARG cc_start: 0.8539 (ptm-80) cc_final: 0.8185 (ttt-90) REVERT: D 704 MET cc_start: 0.8887 (mtt) cc_final: 0.8581 (mtm) REVERT: E 602 MET cc_start: 0.8680 (ttm) cc_final: 0.8251 (ttp) REVERT: E 725 TYR cc_start: 0.6484 (m-80) cc_final: 0.6185 (m-10) outliers start: 63 outliers final: 28 residues processed: 282 average time/residue: 0.5687 time to fit residues: 187.6044 Evaluate side-chains 251 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 466 LYS 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 215 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 500 CYS 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 469 VAL 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 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 724 VAL Chi-restraints excluded: chain E residue 92 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 154 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 295 optimal weight: 5.9990 chunk 30 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 273 optimal weight: 0.3980 chunk 257 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 435 ASN E 584 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.106605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.084534 restraints weight = 41587.090| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.21 r_work: 0.3013 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24893 Z= 0.132 Angle : 0.530 7.419 33889 Z= 0.271 Chirality : 0.047 0.251 3794 Planarity : 0.004 0.048 4501 Dihedral : 4.777 25.543 3358 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.32 % Allowed : 11.43 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.15), residues: 3100 helix: 0.47 (0.25), residues: 449 sheet: -0.73 (0.17), residues: 891 loop : -1.10 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 291 TYR 0.018 0.001 TYR C 523 PHE 0.018 0.001 PHE D 573 TRP 0.012 0.001 TRP A 253 HIS 0.005 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00304 (24888) covalent geometry : angle 0.52913 (33879) SS BOND : bond 0.00316 ( 5) SS BOND : angle 1.29682 ( 10) hydrogen bonds : bond 0.03185 ( 817) hydrogen bonds : angle 5.57410 ( 2343) *********************** 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 303 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 240 time to evaluate : 1.066 Fit side-chains REVERT: A 368 ARG cc_start: 0.8563 (ttp80) cc_final: 0.8295 (ttm170) REVERT: A 466 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8088 (ttmm) REVERT: A 523 TYR cc_start: 0.7691 (m-80) cc_final: 0.7245 (m-80) REVERT: B 359 ASP cc_start: 0.8832 (t0) cc_final: 0.8454 (t0) REVERT: B 499 ASN cc_start: 0.8427 (t0) cc_final: 0.7863 (m110) REVERT: B 598 ASP cc_start: 0.8213 (t0) cc_final: 0.7907 (t0) REVERT: B 693 ASP cc_start: 0.8849 (t0) cc_final: 0.8628 (t0) REVERT: C 704 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8653 (mtm) REVERT: D 112 MET cc_start: 0.8543 (tpp) cc_final: 0.8147 (mmt) REVERT: D 146 LYS cc_start: 0.9256 (tppt) cc_final: 0.8922 (mptt) REVERT: D 215 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.7018 (p90) REVERT: D 359 ASP cc_start: 0.8365 (t0) cc_final: 0.7891 (t0) REVERT: D 403 TYR cc_start: 0.6857 (t80) cc_final: 0.6529 (t80) REVERT: D 411 ASP cc_start: 0.8401 (t0) cc_final: 0.7708 (p0) REVERT: D 435 ASN cc_start: 0.8980 (t0) cc_final: 0.8318 (t0) REVERT: D 704 MET cc_start: 0.8885 (mtt) cc_final: 0.8618 (mtm) REVERT: E 439 GLN cc_start: 0.7514 (tt0) cc_final: 0.7248 (tt0) REVERT: E 481 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8002 (mm-40) REVERT: E 602 MET cc_start: 0.8616 (ttm) cc_final: 0.8185 (ttp) REVERT: E 725 TYR cc_start: 0.6585 (m-80) cc_final: 0.6261 (m-10) REVERT: E 726 TYR cc_start: 0.6925 (m-80) cc_final: 0.6456 (m-80) outliers start: 63 outliers final: 36 residues processed: 274 average time/residue: 0.5985 time to fit residues: 192.4987 Evaluate side-chains 272 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 423 VAL Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 506 VAL 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 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 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 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 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 724 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 MET 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 86 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 246 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 289 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.083987 restraints weight = 41511.415| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.24 r_work: 0.3033 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24893 Z= 0.189 Angle : 0.555 7.602 33889 Z= 0.283 Chirality : 0.048 0.206 3794 Planarity : 0.005 0.048 4501 Dihedral : 4.823 25.715 3358 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.47 % Allowed : 12.65 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.15), residues: 3100 helix: 0.61 (0.25), residues: 449 sheet: -0.62 (0.17), residues: 920 loop : -0.96 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 291 TYR 0.019 0.001 TYR C 523 PHE 0.020 0.002 PHE D 573 TRP 0.011 0.001 TRP A 253 HIS 0.006 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00450 (24888) covalent geometry : angle 0.55458 (33879) SS BOND : bond 0.00190 ( 5) SS BOND : angle 1.41326 ( 10) hydrogen bonds : bond 0.03338 ( 817) hydrogen bonds : angle 5.53539 ( 2343) *********************** 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 306 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 239 time to evaluate : 0.967 Fit side-chains REVERT: A 368 ARG cc_start: 0.8608 (ttp80) cc_final: 0.8331 (ttm170) REVERT: A 523 TYR cc_start: 0.7703 (m-80) cc_final: 0.7309 (m-80) REVERT: B 359 ASP cc_start: 0.8846 (t0) cc_final: 0.8332 (t0) REVERT: B 499 ASN cc_start: 0.8450 (t0) cc_final: 0.7874 (m110) REVERT: B 598 ASP cc_start: 0.8292 (t0) cc_final: 0.8003 (t0) REVERT: C 573 PHE cc_start: 0.9353 (OUTLIER) cc_final: 0.8319 (p90) REVERT: C 633 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.7907 (ttm-80) REVERT: C 704 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8746 (mtt) REVERT: D 112 MET cc_start: 0.8549 (tpp) cc_final: 0.8223 (mmp) REVERT: D 146 LYS cc_start: 0.9276 (ttpt) cc_final: 0.8927 (mptt) REVERT: D 215 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.6999 (p90) REVERT: D 359 ASP cc_start: 0.8409 (t0) cc_final: 0.7909 (t0) REVERT: D 411 ASP cc_start: 0.8371 (t0) cc_final: 0.7679 (p0) REVERT: D 435 ASN cc_start: 0.8963 (t0) cc_final: 0.8318 (t0) REVERT: D 544 ARG cc_start: 0.8613 (ptm-80) cc_final: 0.8279 (ttt-90) REVERT: D 704 MET cc_start: 0.8912 (mtt) cc_final: 0.8634 (mtm) REVERT: E 116 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: E 481 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8014 (mm-40) REVERT: E 602 MET cc_start: 0.8670 (ttm) cc_final: 0.8169 (ttp) REVERT: E 725 TYR cc_start: 0.6523 (m-80) cc_final: 0.6241 (m-10) outliers start: 67 outliers final: 38 residues processed: 278 average time/residue: 0.6026 time to fit residues: 196.5351 Evaluate side-chains 267 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 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 218 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 485 ASP 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 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 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 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 545 MET Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 611 LEU 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 385 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 158 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 255 optimal weight: 8.9990 chunk 242 optimal weight: 6.9990 chunk 281 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN B 490 ASN D 93 ASN E 435 ASN E 537 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.106283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.084091 restraints weight = 41478.828| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.24 r_work: 0.3036 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24893 Z= 0.181 Angle : 0.552 6.774 33889 Z= 0.282 Chirality : 0.047 0.203 3794 Planarity : 0.005 0.048 4501 Dihedral : 4.821 25.519 3358 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.69 % Allowed : 13.39 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.15), residues: 3100 helix: 0.69 (0.25), residues: 449 sheet: -0.49 (0.17), residues: 931 loop : -0.89 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 291 TYR 0.018 0.001 TYR C 523 PHE 0.020 0.002 PHE D 573 TRP 0.012 0.001 TRP A 253 HIS 0.006 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00428 (24888) covalent geometry : angle 0.55195 (33879) SS BOND : bond 0.00196 ( 5) SS BOND : angle 1.38805 ( 10) hydrogen bonds : bond 0.03235 ( 817) hydrogen bonds : angle 5.45062 ( 2343) *********************** 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 304 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 231 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 368 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8346 (ttm170) REVERT: A 492 MET cc_start: 0.8215 (mtm) cc_final: 0.7943 (mtm) REVERT: A 523 TYR cc_start: 0.7678 (m-80) cc_final: 0.7272 (m-80) REVERT: B 359 ASP cc_start: 0.8839 (t0) cc_final: 0.8341 (t0) REVERT: B 499 ASN cc_start: 0.8437 (t0) cc_final: 0.7867 (m110) REVERT: B 598 ASP cc_start: 0.8357 (t0) cc_final: 0.8035 (t0) REVERT: C 352 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8799 (mt) REVERT: C 573 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8292 (p90) REVERT: C 704 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8737 (mtt) REVERT: D 112 MET cc_start: 0.8561 (tpp) cc_final: 0.8197 (mmp) REVERT: D 146 LYS cc_start: 0.9297 (ttpt) cc_final: 0.8938 (mptt) REVERT: D 215 HIS cc_start: 0.7626 (OUTLIER) cc_final: 0.7184 (p90) REVERT: D 240 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7070 (m-30) REVERT: D 359 ASP cc_start: 0.8492 (t0) cc_final: 0.7975 (t0) REVERT: D 411 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7669 (p0) REVERT: D 435 ASN cc_start: 0.8962 (t0) cc_final: 0.8324 (t0) REVERT: E 116 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8310 (tm-30) REVERT: E 481 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8028 (mm-40) REVERT: E 602 MET cc_start: 0.8673 (ttm) cc_final: 0.8163 (ttp) REVERT: E 725 TYR cc_start: 0.6514 (m-80) cc_final: 0.6278 (m-10) outliers start: 73 outliers final: 44 residues processed: 278 average time/residue: 0.5711 time to fit residues: 187.0065 Evaluate side-chains 280 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 300 VAL 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 218 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 435 ASN 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 215 HIS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 352 LEU 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 162 LEU Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 240 ASP 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 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 724 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 116 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 222 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 247 optimal weight: 2.9990 chunk 309 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 290 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN E 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.105752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.083541 restraints weight = 41547.102| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.24 r_work: 0.2982 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24893 Z= 0.210 Angle : 0.566 6.767 33889 Z= 0.289 Chirality : 0.048 0.190 3794 Planarity : 0.005 0.049 4501 Dihedral : 4.877 25.561 3358 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.66 % Allowed : 13.72 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.15), residues: 3100 helix: 0.69 (0.25), residues: 449 sheet: -0.45 (0.17), residues: 928 loop : -0.86 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 291 TYR 0.014 0.001 TYR D 403 PHE 0.020 0.002 PHE D 573 TRP 0.011 0.001 TRP A 253 HIS 0.006 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00500 (24888) covalent geometry : angle 0.56534 (33879) SS BOND : bond 0.00193 ( 5) SS BOND : angle 1.40161 ( 10) hydrogen bonds : bond 0.03301 ( 817) hydrogen bonds : angle 5.47260 ( 2343) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 233 time to evaluate : 1.009 Fit side-chains REVERT: A 368 ARG cc_start: 0.8649 (ttp80) cc_final: 0.8361 (ttm170) REVERT: A 492 MET cc_start: 0.8218 (mtm) cc_final: 0.7986 (mtm) REVERT: A 523 TYR cc_start: 0.7696 (m-80) cc_final: 0.7324 (m-80) REVERT: B 303 MET cc_start: 0.9209 (ttm) cc_final: 0.9008 (ttp) REVERT: B 359 ASP cc_start: 0.8894 (t0) cc_final: 0.8431 (t0) REVERT: B 499 ASN cc_start: 0.8503 (t0) cc_final: 0.7908 (m110) REVERT: B 598 ASP cc_start: 0.8368 (t0) cc_final: 0.8047 (t0) REVERT: C 353 LEU cc_start: 0.9409 (mt) cc_final: 0.9198 (mt) REVERT: C 412 MET cc_start: 0.8968 (ptt) cc_final: 0.8759 (ptt) REVERT: C 573 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.8337 (p90) REVERT: C 704 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8833 (mtt) REVERT: D 112 MET cc_start: 0.8582 (tpp) cc_final: 0.8217 (mmp) REVERT: D 146 LYS cc_start: 0.9313 (ttpt) cc_final: 0.8915 (mptt) REVERT: D 215 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.7154 (p90) REVERT: D 240 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7042 (m-30) REVERT: D 359 ASP cc_start: 0.8533 (t0) cc_final: 0.7996 (t0) REVERT: D 403 TYR cc_start: 0.6843 (OUTLIER) cc_final: 0.6614 (t80) REVERT: D 411 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7625 (p0) REVERT: D 435 ASN cc_start: 0.8997 (t0) cc_final: 0.8378 (t0) REVERT: D 503 PHE cc_start: 0.8222 (m-80) cc_final: 0.7980 (m-80) REVERT: E 116 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: E 481 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8009 (mm-40) REVERT: E 602 MET cc_start: 0.8695 (ttm) cc_final: 0.8167 (ttp) REVERT: E 725 TYR cc_start: 0.6507 (m-80) cc_final: 0.6270 (m-10) outliers start: 72 outliers final: 40 residues processed: 275 average time/residue: 0.5595 time to fit residues: 180.9667 Evaluate side-chains 272 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 300 VAL 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 218 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 489 MET 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 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 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 162 LEU Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 403 TYR 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 583 ILE Chi-restraints excluded: chain D residue 611 LEU 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 116 GLU 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 586 THR 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 73 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 277 optimal weight: 0.3980 chunk 288 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN D 93 ASN E 435 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.108066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.085959 restraints weight = 41336.340| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.25 r_work: 0.3005 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24893 Z= 0.141 Angle : 0.541 9.090 33889 Z= 0.276 Chirality : 0.046 0.204 3794 Planarity : 0.004 0.050 4501 Dihedral : 4.744 24.389 3358 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.47 % Allowed : 13.83 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3100 helix: 0.83 (0.25), residues: 461 sheet: -0.35 (0.17), residues: 918 loop : -0.76 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 291 TYR 0.014 0.001 TYR D 403 PHE 0.018 0.001 PHE D 573 TRP 0.012 0.001 TRP A 253 HIS 0.005 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00332 (24888) covalent geometry : angle 0.54071 (33879) SS BOND : bond 0.00214 ( 5) SS BOND : angle 1.30406 ( 10) hydrogen bonds : bond 0.03038 ( 817) hydrogen bonds : angle 5.29159 ( 2343) *********************** 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 306 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 239 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 492 MET cc_start: 0.8209 (mtm) cc_final: 0.7964 (mtm) REVERT: A 523 TYR cc_start: 0.7652 (m-80) cc_final: 0.7349 (m-10) REVERT: B 303 MET cc_start: 0.9177 (ttm) cc_final: 0.8967 (ttt) REVERT: B 359 ASP cc_start: 0.8850 (t0) cc_final: 0.8513 (t0) REVERT: B 499 ASN cc_start: 0.8440 (t0) cc_final: 0.7908 (m110) REVERT: B 598 ASP cc_start: 0.8378 (t0) cc_final: 0.8057 (t0) REVERT: C 353 LEU cc_start: 0.9411 (mt) cc_final: 0.9197 (mt) REVERT: C 573 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.8256 (p90) REVERT: D 112 MET cc_start: 0.8569 (tpp) cc_final: 0.8161 (mmp) REVERT: D 146 LYS cc_start: 0.9306 (ttpt) cc_final: 0.8920 (mptt) REVERT: D 215 HIS cc_start: 0.7612 (OUTLIER) cc_final: 0.7137 (p90) REVERT: D 240 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7082 (m-30) REVERT: D 403 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.6541 (t80) REVERT: D 411 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7649 (p0) REVERT: D 435 ASN cc_start: 0.8967 (t0) cc_final: 0.8352 (t0) REVERT: D 492 MET cc_start: 0.8572 (mtm) cc_final: 0.7612 (mtm) REVERT: D 638 PRO cc_start: 0.7943 (Cg_endo) cc_final: 0.7626 (Cg_exo) REVERT: D 704 MET cc_start: 0.8866 (mtt) cc_final: 0.8603 (mtm) REVERT: E 116 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: E 481 GLN cc_start: 0.8355 (tt0) cc_final: 0.8023 (mm-40) REVERT: E 485 ASP cc_start: 0.7741 (t0) cc_final: 0.7484 (t0) REVERT: E 602 MET cc_start: 0.8665 (ttm) cc_final: 0.8157 (ttp) REVERT: E 673 ASP cc_start: 0.7127 (m-30) cc_final: 0.6594 (p0) outliers start: 67 outliers final: 45 residues processed: 281 average time/residue: 0.5358 time to fit residues: 177.7380 Evaluate side-chains 282 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 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 435 ASN Chi-restraints excluded: chain B residue 489 MET 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 708 VAL 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 469 VAL Chi-restraints excluded: chain C residue 496 SER 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 D residue 102 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 234 VAL Chi-restraints excluded: chain D residue 240 ASP 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 403 TYR 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 573 PHE Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 611 LEU 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 116 GLU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 586 THR 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 46 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 252 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 181 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN D 93 ASN E 160 ASN E 435 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.106926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.084861 restraints weight = 41529.164| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.21 r_work: 0.3056 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24893 Z= 0.136 Angle : 0.547 8.137 33889 Z= 0.278 Chirality : 0.047 0.232 3794 Planarity : 0.005 0.052 4501 Dihedral : 4.741 29.344 3358 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.36 % Allowed : 14.39 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 3100 helix: 0.93 (0.25), residues: 461 sheet: -0.24 (0.17), residues: 923 loop : -0.70 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 291 TYR 0.014 0.001 TYR D 403 PHE 0.017 0.001 PHE D 573 TRP 0.012 0.001 TRP A 253 HIS 0.005 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00320 (24888) covalent geometry : angle 0.54506 (33879) SS BOND : bond 0.00284 ( 5) SS BOND : angle 2.69555 ( 10) hydrogen bonds : bond 0.02978 ( 817) hydrogen bonds : angle 5.22308 ( 2343) *********************** 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 300 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 236 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 TYR cc_start: 0.7635 (m-80) cc_final: 0.7343 (m-10) REVERT: B 303 MET cc_start: 0.9161 (ttm) cc_final: 0.8956 (ttt) REVERT: B 359 ASP cc_start: 0.8813 (t0) cc_final: 0.8494 (t0) REVERT: B 499 ASN cc_start: 0.8460 (t0) cc_final: 0.7900 (m110) REVERT: B 598 ASP cc_start: 0.8355 (t0) cc_final: 0.8014 (t0) REVERT: B 693 ASP cc_start: 0.8813 (t0) cc_final: 0.8594 (t0) REVERT: C 353 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9191 (mt) REVERT: C 573 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.8225 (p90) REVERT: C 704 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8685 (mtt) REVERT: D 112 MET cc_start: 0.8573 (tpp) cc_final: 0.8178 (mmp) REVERT: D 146 LYS cc_start: 0.9302 (ttpt) cc_final: 0.8960 (mptt) REVERT: D 215 HIS cc_start: 0.7612 (OUTLIER) cc_final: 0.7138 (p90) REVERT: D 240 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7088 (m-30) REVERT: D 403 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.6586 (t80) REVERT: D 435 ASN cc_start: 0.8951 (t0) cc_final: 0.8338 (t0) REVERT: D 492 MET cc_start: 0.8631 (mtm) cc_final: 0.7781 (mtm) REVERT: D 638 PRO cc_start: 0.8034 (Cg_endo) cc_final: 0.7740 (Cg_exo) REVERT: D 704 MET cc_start: 0.8874 (mtt) cc_final: 0.8629 (mtm) REVERT: E 116 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8296 (tm-30) REVERT: E 481 GLN cc_start: 0.8376 (tt0) cc_final: 0.8056 (mm-40) REVERT: E 485 ASP cc_start: 0.7705 (t0) cc_final: 0.7468 (t0) REVERT: E 602 MET cc_start: 0.8650 (ttm) cc_final: 0.8156 (ttp) REVERT: E 673 ASP cc_start: 0.7180 (m-30) cc_final: 0.6639 (p0) outliers start: 64 outliers final: 43 residues processed: 274 average time/residue: 0.5729 time to fit residues: 184.1649 Evaluate side-chains 277 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 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 218 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 489 MET 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 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 353 LEU 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 162 LEU Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 240 ASP 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 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 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 724 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 586 THR 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 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.4980 chunk 214 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 151 optimal weight: 0.1980 chunk 220 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 415 ASN A 507 GLN D 93 ASN E 435 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.108349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.086177 restraints weight = 41493.370| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.20 r_work: 0.3045 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24893 Z= 0.129 Angle : 0.537 9.150 33889 Z= 0.273 Chirality : 0.046 0.196 3794 Planarity : 0.005 0.057 4501 Dihedral : 4.651 24.660 3358 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.99 % Allowed : 15.09 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 3100 helix: 1.04 (0.25), residues: 461 sheet: -0.15 (0.17), residues: 923 loop : -0.65 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 291 TYR 0.014 0.001 TYR D 403 PHE 0.017 0.001 PHE B 573 TRP 0.012 0.001 TRP A 253 HIS 0.004 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00305 (24888) covalent geometry : angle 0.53620 (33879) SS BOND : bond 0.00403 ( 5) SS BOND : angle 1.94659 ( 10) hydrogen bonds : bond 0.02916 ( 817) hydrogen bonds : angle 5.13789 ( 2343) ********************** 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 285 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 ARG cc_start: 0.8575 (ttp-110) cc_final: 0.8268 (ptp90) REVERT: A 523 TYR cc_start: 0.7639 (m-80) cc_final: 0.7295 (m-80) REVERT: B 359 ASP cc_start: 0.8823 (t0) cc_final: 0.8333 (t0) REVERT: B 499 ASN cc_start: 0.8446 (t0) cc_final: 0.7869 (m110) REVERT: B 598 ASP cc_start: 0.8347 (t0) cc_final: 0.8033 (t0) REVERT: B 693 ASP cc_start: 0.8826 (t0) cc_final: 0.8599 (t0) REVERT: C 352 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8798 (mt) REVERT: C 573 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8198 (p90) REVERT: C 704 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8629 (mtm) REVERT: D 112 MET cc_start: 0.8565 (tpp) cc_final: 0.8203 (mmp) REVERT: D 146 LYS cc_start: 0.9300 (ttpt) cc_final: 0.8947 (mptt) REVERT: D 215 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.7127 (p90) REVERT: D 240 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7073 (m-30) REVERT: D 435 ASN cc_start: 0.8940 (t0) cc_final: 0.8340 (t0) REVERT: D 492 MET cc_start: 0.8673 (mtm) cc_final: 0.7820 (mtm) REVERT: D 638 PRO cc_start: 0.8043 (Cg_endo) cc_final: 0.7752 (Cg_exo) REVERT: D 704 MET cc_start: 0.8879 (mtt) cc_final: 0.8635 (mtm) REVERT: E 116 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: E 481 GLN cc_start: 0.8361 (tt0) cc_final: 0.8043 (mm-40) REVERT: E 485 ASP cc_start: 0.7642 (t0) cc_final: 0.7397 (t0) REVERT: E 602 MET cc_start: 0.8710 (ttm) cc_final: 0.8189 (ttp) REVERT: E 673 ASP cc_start: 0.7156 (m-30) cc_final: 0.6660 (p0) REVERT: E 719 LEU cc_start: 0.8263 (mm) cc_final: 0.7923 (mm) outliers start: 54 outliers final: 38 residues processed: 265 average time/residue: 0.5396 time to fit residues: 167.7979 Evaluate side-chains 268 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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 218 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 489 MET 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 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 352 LEU 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 234 VAL Chi-restraints excluded: chain D residue 240 ASP 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 583 ILE Chi-restraints excluded: chain D residue 611 LEU 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 467 THR Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 586 THR 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 130 optimal weight: 0.0870 chunk 236 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 233 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 415 ASN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN E 435 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.085781 restraints weight = 41415.764| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.20 r_work: 0.3034 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24893 Z= 0.146 Angle : 0.546 9.904 33889 Z= 0.277 Chirality : 0.047 0.185 3794 Planarity : 0.005 0.056 4501 Dihedral : 4.659 23.652 3358 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.10 % Allowed : 15.16 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.15), residues: 3100 helix: 1.04 (0.25), residues: 461 sheet: -0.12 (0.17), residues: 929 loop : -0.62 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 291 TYR 0.011 0.001 TYR D 403 PHE 0.017 0.001 PHE B 573 TRP 0.011 0.001 TRP A 253 HIS 0.005 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00347 (24888) covalent geometry : angle 0.54487 (33879) SS BOND : bond 0.00443 ( 5) SS BOND : angle 1.66336 ( 10) hydrogen bonds : bond 0.02979 ( 817) hydrogen bonds : angle 5.15302 ( 2343) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7682.45 seconds wall clock time: 131 minutes 43.48 seconds (7903.48 seconds total)