Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 06:00:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/08_2023/7ras_24385_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/08_2023/7ras_24385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/08_2023/7ras_24385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/08_2023/7ras_24385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/08_2023/7ras_24385_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/08_2023/7ras_24385_updated.pdb" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.026 sd= 0.082 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 116 5.16 5 C 13072 2.51 5 N 3272 2.21 5 O 3540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 698": "NH1" <-> "NH2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 698": "NH1" <-> "NH2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 698": "NH1" <-> "NH2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 20000 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4964 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 596} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4964 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 596} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4964 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 596} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4964 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 596} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'A0O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'A0O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'A0O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'A0O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.91, per 1000 atoms: 0.50 Number of scatterers: 20000 At special positions: 0 Unit cell: (136.95, 136.95, 117.86, 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 116 16.00 O 3540 8.00 N 3272 7.00 C 13072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.41 Conformation dependent library (CDL) restraints added in 3.1 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 4 sheets defined 58.0% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 116 through 128 removed outlier: 3.540A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.768A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.845A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 228 through 237 removed outlier: 3.776A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 3.788A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 299 through 305 Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.756A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.692A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.652A pdb=" N THR A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 4.124A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 459 removed outlier: 4.278A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.648A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 542 removed outlier: 4.133A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 565 removed outlier: 3.934A pdb=" N ALA A 549 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS A 550 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 551 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 556 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 557 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP A 559 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 562 " --> pdb=" O TRP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 577 through 607 removed outlier: 3.510A pdb=" N VAL A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.915A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 678 removed outlier: 3.572A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 706 removed outlier: 3.621A pdb=" N SER A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'B' and resid 116 through 128 removed outlier: 3.539A pdb=" N LYS B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.767A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.845A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 228 through 237 removed outlier: 3.775A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 3.789A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 299 through 305 Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.756A pdb=" N ILE B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 355 through 361 removed outlier: 3.692A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.651A pdb=" N THR B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 435 removed outlier: 4.124A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 459 removed outlier: 4.278A pdb=" N PHE B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 507 removed outlier: 3.648A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 542 removed outlier: 4.132A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 565 removed outlier: 3.933A pdb=" N ALA B 549 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N CYS B 550 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 551 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 556 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 557 " --> pdb=" O ALA B 554 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP B 559 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 562 " --> pdb=" O TRP B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 577 through 607 removed outlier: 3.509A pdb=" N VAL B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 removed outlier: 3.915A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 633 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 678 removed outlier: 3.572A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 706 removed outlier: 3.620A pdb=" N SER B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 690 " --> pdb=" O LYS B 686 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'C' and resid 116 through 128 removed outlier: 3.539A pdb=" N LYS C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 171 through 177 removed outlier: 3.767A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.846A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.775A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 3.789A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 299 through 305 Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.756A pdb=" N ILE C 324 " --> pdb=" O MET C 320 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.692A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 360 " --> pdb=" O ILE C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.652A pdb=" N THR C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 435 removed outlier: 4.124A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 459 removed outlier: 4.278A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 507 removed outlier: 3.648A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 542 removed outlier: 4.133A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 565 removed outlier: 3.933A pdb=" N ALA C 549 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS C 550 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 551 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 556 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 557 " --> pdb=" O ALA C 554 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP C 559 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C 562 " --> pdb=" O TRP C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 577 through 607 removed outlier: 3.509A pdb=" N VAL C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 3.916A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE C 633 " --> pdb=" O VAL C 629 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 678 removed outlier: 3.573A pdb=" N LEU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 706 removed outlier: 3.620A pdb=" N SER C 685 " --> pdb=" O VAL C 681 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 690 " --> pdb=" O LYS C 686 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'D' and resid 116 through 128 removed outlier: 3.540A pdb=" N LYS D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 147 Processing helix chain 'D' and resid 156 through 160 Processing helix chain 'D' and resid 171 through 177 removed outlier: 3.768A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.845A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 228 through 237 removed outlier: 3.775A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 234 " --> pdb=" O ILE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.790A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 283 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 299 through 305 Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.757A pdb=" N ILE D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 350 Processing helix chain 'D' and resid 355 through 361 removed outlier: 3.691A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 360 " --> pdb=" O ILE D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 407 Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.651A pdb=" N THR D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 435 removed outlier: 4.125A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 459 removed outlier: 4.278A pdb=" N PHE D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR D 456 " --> pdb=" O ASN D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 507 removed outlier: 3.648A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 542 removed outlier: 4.132A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 565 removed outlier: 3.934A pdb=" N ALA D 549 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS D 550 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 551 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 556 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 557 " --> pdb=" O ALA D 554 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP D 559 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET D 562 " --> pdb=" O TRP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 573 No H-bonds generated for 'chain 'D' and resid 571 through 573' Processing helix chain 'D' and resid 577 through 607 removed outlier: 3.509A pdb=" N VAL D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 removed outlier: 3.915A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 633 " --> pdb=" O VAL D 629 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 678 removed outlier: 3.572A pdb=" N LEU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 706 removed outlier: 3.620A pdb=" N SER D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 690 " --> pdb=" O LYS D 686 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 714 Processing sheet with id= A, first strand: chain 'A' and resid 719 through 721 removed outlier: 3.554A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 719 through 721 removed outlier: 3.554A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 719 through 721 removed outlier: 3.554A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 719 through 721 removed outlier: 3.554A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2376 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: 5.28 Time building geometry restraints manager: 8.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3216 1.32 - 1.44: 5536 1.44 - 1.56: 11468 1.56 - 1.69: 8 1.69 - 1.81: 196 Bond restraints: 20424 Sorted by residual: bond pdb=" C07 A0O C 902 " pdb=" C12 A0O C 902 " ideal model delta sigma weight residual 1.430 1.647 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C07 A0O A 902 " pdb=" C12 A0O A 902 " ideal model delta sigma weight residual 1.430 1.646 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C07 A0O D 902 " pdb=" C12 A0O D 902 " ideal model delta sigma weight residual 1.430 1.646 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C07 A0O B 902 " pdb=" C12 A0O B 902 " ideal model delta sigma weight residual 1.430 1.646 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C07 A0O B 901 " pdb=" C12 A0O B 901 " ideal model delta sigma weight residual 1.430 1.645 -0.215 2.00e-02 2.50e+03 1.16e+02 ... (remaining 20419 not shown) Histogram of bond angle deviations from ideal: 96.81 - 106.40: 384 106.40 - 116.00: 12659 116.00 - 125.60: 14216 125.60 - 135.19: 353 135.19 - 144.79: 8 Bond angle restraints: 27620 Sorted by residual: angle pdb=" C04 A0O D 902 " pdb=" C06 A0O D 902 " pdb=" O01 A0O D 902 " ideal model delta sigma weight residual 117.13 144.79 -27.66 3.00e+00 1.11e-01 8.50e+01 angle pdb=" C04 A0O C 902 " pdb=" C06 A0O C 902 " pdb=" O01 A0O C 902 " ideal model delta sigma weight residual 117.13 144.76 -27.63 3.00e+00 1.11e-01 8.49e+01 angle pdb=" C04 A0O B 902 " pdb=" C06 A0O B 902 " pdb=" O01 A0O B 902 " ideal model delta sigma weight residual 117.13 144.72 -27.59 3.00e+00 1.11e-01 8.46e+01 angle pdb=" C04 A0O B 901 " pdb=" C06 A0O B 901 " pdb=" O01 A0O B 901 " ideal model delta sigma weight residual 117.13 144.72 -27.59 3.00e+00 1.11e-01 8.46e+01 angle pdb=" C04 A0O A 902 " pdb=" C06 A0O A 902 " pdb=" O01 A0O A 902 " ideal model delta sigma weight residual 117.13 144.69 -27.56 3.00e+00 1.11e-01 8.44e+01 ... (remaining 27615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 11136 15.14 - 30.29: 731 30.29 - 45.43: 217 45.43 - 60.57: 24 60.57 - 75.72: 16 Dihedral angle restraints: 12124 sinusoidal: 4948 harmonic: 7176 Sorted by residual: dihedral pdb=" CA ASP B 414 " pdb=" C ASP B 414 " pdb=" N ASN B 415 " pdb=" CA ASN B 415 " ideal model delta harmonic sigma weight residual 180.00 137.79 42.21 0 5.00e+00 4.00e-02 7.13e+01 dihedral pdb=" CA ASP C 414 " pdb=" C ASP C 414 " pdb=" N ASN C 415 " pdb=" CA ASN C 415 " ideal model delta harmonic sigma weight residual 180.00 137.79 42.21 0 5.00e+00 4.00e-02 7.13e+01 dihedral pdb=" CA ASP D 414 " pdb=" C ASP D 414 " pdb=" N ASN D 415 " pdb=" CA ASN D 415 " ideal model delta harmonic sigma weight residual 180.00 137.83 42.17 0 5.00e+00 4.00e-02 7.11e+01 ... (remaining 12121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2011 0.040 - 0.080: 899 0.080 - 0.119: 168 0.119 - 0.159: 46 0.159 - 0.199: 28 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CA GLU B 423 " pdb=" N GLU B 423 " pdb=" C GLU B 423 " pdb=" CB GLU B 423 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA VAL D 154 " pdb=" N VAL D 154 " pdb=" C VAL D 154 " pdb=" CB VAL D 154 " both_signs ideal model delta sigma weight residual False 2.44 2.24 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CA VAL C 154 " pdb=" N VAL C 154 " pdb=" C VAL C 154 " pdb=" CB VAL C 154 " both_signs ideal model delta sigma weight residual False 2.44 2.24 0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 3149 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 752 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.28e+00 pdb=" N PRO D 753 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 753 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 753 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 752 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.26e+00 pdb=" N PRO A 753 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 753 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 753 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 752 " -0.044 5.00e-02 4.00e+02 6.72e-02 7.23e+00 pdb=" N PRO C 753 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 753 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 753 " -0.037 5.00e-02 4.00e+02 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5840 2.81 - 3.33: 18621 3.33 - 3.85: 31345 3.85 - 4.38: 37311 4.38 - 4.90: 61983 Nonbonded interactions: 155100 Sorted by model distance: nonbonded pdb=" OG1 THR A 399 " pdb=" O ASN A 401 " model vdw 2.283 2.440 nonbonded pdb=" OG1 THR D 399 " pdb=" O ASN D 401 " model vdw 2.283 2.440 nonbonded pdb=" OG1 THR C 399 " pdb=" O ASN C 401 " model vdw 2.283 2.440 nonbonded pdb=" OG1 THR B 399 " pdb=" O ASN B 401 " model vdw 2.284 2.440 nonbonded pdb=" OD1 ASP C 322 " pdb=" OH TYR C 359 " model vdw 2.285 2.440 ... (remaining 155095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.940 Check model and map are aligned: 0.310 Set scattering table: 0.160 Process input model: 49.670 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.100 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.010 0.217 20424 Z= 0.646 Angle : 1.327 27.659 27620 Z= 0.639 Chirality : 0.048 0.199 3152 Planarity : 0.006 0.067 3420 Dihedral : 11.678 75.715 7460 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.31 % Favored : 93.19 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.09 (0.09), residues: 2408 helix: -4.23 (0.05), residues: 1464 sheet: -1.41 (0.43), residues: 92 loop : -3.61 (0.15), residues: 852 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 466 time to evaluate : 2.400 Fit side-chains outliers start: 24 outliers final: 8 residues processed: 490 average time/residue: 0.3019 time to fit residues: 229.1067 Evaluate side-chains 250 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 242 time to evaluate : 2.733 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1749 time to fit residues: 6.4663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.8980 chunk 184 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 191 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 216 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 671 ASN A 735 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 645 GLN B 671 ASN B 735 ASN C 178 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 GLN C 671 ASN C 735 ASN D 178 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN D 671 ASN D 735 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 20424 Z= 0.220 Angle : 0.717 12.857 27620 Z= 0.348 Chirality : 0.040 0.219 3152 Planarity : 0.005 0.049 3420 Dihedral : 6.067 46.973 2692 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.49 % Favored : 95.18 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.14), residues: 2408 helix: -1.66 (0.11), residues: 1492 sheet: -0.78 (0.46), residues: 92 loop : -3.41 (0.16), residues: 824 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 306 time to evaluate : 2.602 Fit side-chains outliers start: 60 outliers final: 10 residues processed: 356 average time/residue: 0.2910 time to fit residues: 164.6020 Evaluate side-chains 241 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 231 time to evaluate : 2.368 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1998 time to fit residues: 6.8499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 239 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 178 optimal weight: 0.0060 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 197 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN C 143 GLN C 197 ASN C 216 GLN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN D 143 GLN D 197 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 20424 Z= 0.240 Angle : 0.661 12.638 27620 Z= 0.320 Chirality : 0.040 0.244 3152 Planarity : 0.004 0.041 3420 Dihedral : 5.777 49.726 2692 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.48 % Favored : 94.35 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.15), residues: 2408 helix: -0.28 (0.13), residues: 1488 sheet: -0.44 (0.46), residues: 92 loop : -3.27 (0.17), residues: 828 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 248 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 17 residues processed: 295 average time/residue: 0.2721 time to fit residues: 131.8145 Evaluate side-chains 218 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 201 time to evaluate : 2.367 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1789 time to fit residues: 8.9516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 235 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN B 143 GLN B 197 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN D 216 GLN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 20424 Z= 0.371 Angle : 0.714 11.919 27620 Z= 0.351 Chirality : 0.043 0.230 3152 Planarity : 0.004 0.033 3420 Dihedral : 5.908 51.603 2692 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.81 % Favored : 94.02 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.16), residues: 2408 helix: 0.22 (0.13), residues: 1488 sheet: -0.45 (0.47), residues: 92 loop : -3.17 (0.17), residues: 828 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 219 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 16 residues processed: 264 average time/residue: 0.2736 time to fit residues: 118.7819 Evaluate side-chains 217 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 201 time to evaluate : 2.422 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1778 time to fit residues: 8.5399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 201 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 chunk 59 optimal weight: 0.0570 overall best weight: 2.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 452 ASN ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN D 452 ASN ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 20424 Z= 0.234 Angle : 0.627 11.522 27620 Z= 0.306 Chirality : 0.040 0.195 3152 Planarity : 0.003 0.029 3420 Dihedral : 5.536 51.212 2692 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.11 % Favored : 94.73 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2408 helix: 0.46 (0.13), residues: 1492 sheet: -0.35 (0.47), residues: 92 loop : -3.09 (0.18), residues: 824 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 215 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 18 residues processed: 254 average time/residue: 0.2860 time to fit residues: 121.4500 Evaluate side-chains 216 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 2.510 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2008 time to fit residues: 10.1752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 236 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 0.0020 chunk 123 optimal weight: 8.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 20424 Z= 0.183 Angle : 0.635 15.258 27620 Z= 0.296 Chirality : 0.039 0.189 3152 Planarity : 0.003 0.029 3420 Dihedral : 5.310 52.079 2692 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.52 % Favored : 94.44 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2408 helix: 0.59 (0.14), residues: 1476 sheet: -0.32 (0.46), residues: 92 loop : -3.04 (0.18), residues: 840 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 221 time to evaluate : 2.285 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 11 residues processed: 250 average time/residue: 0.2651 time to fit residues: 109.9248 Evaluate side-chains 202 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 191 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1768 time to fit residues: 6.8852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 134 optimal weight: 0.0070 chunk 172 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 198 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 108 optimal weight: 30.0000 overall best weight: 1.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 160 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 20424 Z= 0.181 Angle : 0.650 13.998 27620 Z= 0.300 Chirality : 0.039 0.254 3152 Planarity : 0.003 0.027 3420 Dihedral : 5.217 54.167 2692 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.36 % Favored : 94.48 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.17), residues: 2408 helix: 0.63 (0.13), residues: 1492 sheet: -0.21 (0.46), residues: 92 loop : -2.93 (0.18), residues: 824 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 221 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 244 average time/residue: 0.2816 time to fit residues: 111.5862 Evaluate side-chains 205 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 195 time to evaluate : 2.631 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1825 time to fit residues: 6.6827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.9980 chunk 93 optimal weight: 0.0470 chunk 140 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 20424 Z= 0.145 Angle : 0.652 14.412 27620 Z= 0.299 Chirality : 0.039 0.374 3152 Planarity : 0.003 0.027 3420 Dihedral : 5.014 52.579 2692 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.44 % Favored : 95.39 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2408 helix: 0.80 (0.13), residues: 1480 sheet: 0.04 (0.48), residues: 92 loop : -2.78 (0.18), residues: 836 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 250 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 255 average time/residue: 0.2977 time to fit residues: 121.0627 Evaluate side-chains 213 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 208 time to evaluate : 2.148 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1901 time to fit residues: 4.7734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 67 optimal weight: 0.5980 chunk 198 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 218 optimal weight: 20.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 20424 Z= 0.162 Angle : 0.652 13.679 27620 Z= 0.300 Chirality : 0.039 0.233 3152 Planarity : 0.003 0.027 3420 Dihedral : 4.993 52.321 2692 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.98 % Favored : 94.85 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.17), residues: 2408 helix: 0.89 (0.14), residues: 1468 sheet: 0.06 (0.49), residues: 92 loop : -2.76 (0.18), residues: 848 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 217 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 222 average time/residue: 0.2902 time to fit residues: 104.2894 Evaluate side-chains 214 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 204 time to evaluate : 2.439 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1907 time to fit residues: 6.9973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.9990 chunk 231 optimal weight: 20.0000 chunk 141 optimal weight: 0.0060 chunk 109 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 243 optimal weight: 0.8980 chunk 223 optimal weight: 7.9990 chunk 193 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 20424 Z= 0.175 Angle : 0.665 13.373 27620 Z= 0.305 Chirality : 0.040 0.224 3152 Planarity : 0.003 0.026 3420 Dihedral : 4.999 51.960 2692 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.86 % Favored : 94.98 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.17), residues: 2408 helix: 0.85 (0.14), residues: 1480 sheet: 0.10 (0.49), residues: 92 loop : -2.82 (0.18), residues: 836 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 209 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 212 average time/residue: 0.2832 time to fit residues: 98.3364 Evaluate side-chains 209 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 206 time to evaluate : 2.353 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1784 time to fit residues: 4.2928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 178 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 193 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 695 GLN D 695 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.141634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.103304 restraints weight = 41091.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.106791 restraints weight = 21468.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.109086 restraints weight = 14470.120| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 20424 Z= 0.149 Angle : 0.666 13.108 27620 Z= 0.304 Chirality : 0.039 0.225 3152 Planarity : 0.003 0.027 3420 Dihedral : 4.850 51.703 2692 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.69 % Favored : 95.14 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2408 helix: 0.88 (0.14), residues: 1504 sheet: 0.06 (0.49), residues: 92 loop : -2.83 (0.18), residues: 812 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3454.64 seconds wall clock time: 64 minutes 19.58 seconds (3859.58 seconds total)