Starting phenix.real_space_refine on Wed Apr 10 16:21:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/04_2024/7ras_24385_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/04_2024/7ras_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_24385/04_2024/7ras_24385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/04_2024/7ras_24385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/04_2024/7ras_24385_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/04_2024/7ras_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 10.57, per 1000 atoms: 0.53 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: 7.05 Conformation dependent library (CDL) restraints added in 3.5 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: 4.44 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: 5.08 Time building geometry restraints manager: 7.70 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: 225 45.43 - 60.57: 24 60.57 - 75.72: 24 Dihedral angle restraints: 12140 sinusoidal: 4964 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 12137 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: 1.790 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: 6.100 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 51.170 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.120 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.740 ------------------------------------------------------------------------------- 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 : 11.929 75.715 7476 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 % Allowed : 7.41 % Favored : 91.48 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 692 HIS 0.011 0.002 HIS A 417 PHE 0.021 0.002 PHE D 261 TYR 0.020 0.003 TYR A 565 ARG 0.013 0.001 ARG D 696 *********************** 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 : 2.354 Fit side-chains REVERT: A 404 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7567 (mt) REVERT: A 418 GLU cc_start: 0.8162 (tp30) cc_final: 0.7841 (tp30) REVERT: A 436 PHE cc_start: 0.7828 (m-10) cc_final: 0.7587 (m-10) REVERT: A 449 PHE cc_start: 0.8080 (t80) cc_final: 0.7834 (t80) REVERT: A 489 PHE cc_start: 0.8454 (t80) cc_final: 0.8179 (t80) REVERT: A 591 LEU cc_start: 0.9324 (mm) cc_final: 0.9101 (pp) REVERT: A 650 TYR cc_start: 0.6730 (m-80) cc_final: 0.6450 (m-80) REVERT: A 695 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8195 (mm-40) REVERT: B 205 ASN cc_start: 0.8430 (m-40) cc_final: 0.7884 (t0) REVERT: B 404 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7713 (mt) REVERT: B 418 GLU cc_start: 0.8065 (tp30) cc_final: 0.7747 (tp30) REVERT: B 449 PHE cc_start: 0.8045 (t80) cc_final: 0.7837 (t80) REVERT: B 489 PHE cc_start: 0.8547 (t80) cc_final: 0.8260 (t80) REVERT: B 550 CYS cc_start: 0.8448 (m) cc_final: 0.7615 (m) REVERT: B 650 TYR cc_start: 0.6843 (m-80) cc_final: 0.6503 (m-80) REVERT: B 669 LEU cc_start: 0.9544 (tp) cc_final: 0.9341 (tt) REVERT: B 695 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8263 (tp40) REVERT: C 404 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7628 (mt) REVERT: C 418 GLU cc_start: 0.8169 (tp30) cc_final: 0.7868 (tp30) REVERT: C 449 PHE cc_start: 0.8094 (t80) cc_final: 0.7834 (t80) REVERT: C 591 LEU cc_start: 0.9322 (mm) cc_final: 0.9085 (pp) REVERT: C 650 TYR cc_start: 0.6653 (m-80) cc_final: 0.6388 (m-80) REVERT: C 695 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8214 (tp40) REVERT: D 404 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7611 (mt) REVERT: D 418 GLU cc_start: 0.8145 (tp30) cc_final: 0.7807 (tp30) REVERT: D 436 PHE cc_start: 0.7808 (m-10) cc_final: 0.7575 (m-10) REVERT: D 449 PHE cc_start: 0.8093 (t80) cc_final: 0.7825 (t80) REVERT: D 489 PHE cc_start: 0.8471 (t80) cc_final: 0.8222 (t80) REVERT: D 550 CYS cc_start: 0.8395 (m) cc_final: 0.7713 (m) REVERT: D 591 LEU cc_start: 0.9309 (mm) cc_final: 0.9085 (pp) REVERT: D 650 TYR cc_start: 0.6776 (m-80) cc_final: 0.6476 (m-80) REVERT: D 695 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8216 (tp40) outliers start: 24 outliers final: 8 residues processed: 490 average time/residue: 0.3062 time to fit residues: 231.7259 Evaluate side-chains 259 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 247 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 404 LEU 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: 10.0000 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: 1.9990 chunk 221 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 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 216 GLN ** 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: 0.7989 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20424 Z= 0.222 Angle : 0.698 12.761 27620 Z= 0.343 Chirality : 0.039 0.221 3152 Planarity : 0.005 0.048 3420 Dihedral : 6.776 50.198 2732 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.32 % Favored : 95.35 % Rotamer: Outliers : 3.19 % Allowed : 13.10 % Favored : 83.70 % 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: -3.38 (0.14), residues: 2408 helix: -1.62 (0.11), residues: 1488 sheet: -0.78 (0.46), residues: 92 loop : -3.44 (0.16), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 493 HIS 0.006 0.001 HIS B 417 PHE 0.013 0.001 PHE C 633 TYR 0.018 0.001 TYR D 321 ARG 0.004 0.000 ARG A 371 *********************** 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 382 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 313 time to evaluate : 2.061 Fit side-chains revert: symmetry clash REVERT: A 173 MET cc_start: 0.8744 (mtp) cc_final: 0.8544 (mtm) REVERT: A 404 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7856 (mt) REVERT: A 418 GLU cc_start: 0.8100 (tp30) cc_final: 0.7758 (tp30) REVERT: A 430 HIS cc_start: 0.7599 (t70) cc_final: 0.7046 (t70) REVERT: A 479 MET cc_start: 0.6182 (mpp) cc_final: 0.5936 (mpp) REVERT: A 493 TRP cc_start: 0.8159 (t-100) cc_final: 0.7821 (t-100) REVERT: A 521 TRP cc_start: 0.7395 (t60) cc_final: 0.6463 (t60) REVERT: A 532 LEU cc_start: 0.8903 (tp) cc_final: 0.8565 (tp) REVERT: A 550 CYS cc_start: 0.8105 (m) cc_final: 0.7748 (t) REVERT: A 555 MET cc_start: 0.8720 (ptp) cc_final: 0.8480 (ptp) REVERT: A 574 MET cc_start: 0.8154 (tpp) cc_final: 0.7798 (tpp) REVERT: A 650 TYR cc_start: 0.6632 (m-80) cc_final: 0.6398 (m-80) REVERT: B 160 HIS cc_start: 0.8083 (m-70) cc_final: 0.7788 (m-70) REVERT: B 196 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8390 (mt-10) REVERT: B 221 ILE cc_start: 0.8860 (mm) cc_final: 0.8495 (mt) REVERT: B 404 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8022 (mt) REVERT: B 418 GLU cc_start: 0.7992 (tp30) cc_final: 0.7664 (tp30) REVERT: B 430 HIS cc_start: 0.7540 (t70) cc_final: 0.7048 (t70) REVERT: B 449 PHE cc_start: 0.8110 (t80) cc_final: 0.7788 (t80) REVERT: B 461 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.7093 (t80) REVERT: B 479 MET cc_start: 0.6121 (mpp) cc_final: 0.5863 (mpp) REVERT: B 521 TRP cc_start: 0.7426 (t60) cc_final: 0.6519 (t60) REVERT: B 532 LEU cc_start: 0.8888 (tp) cc_final: 0.8665 (tp) REVERT: B 550 CYS cc_start: 0.8075 (m) cc_final: 0.7854 (t) REVERT: B 555 MET cc_start: 0.8581 (ptp) cc_final: 0.8380 (ptp) REVERT: B 562 MET cc_start: 0.8513 (tpp) cc_final: 0.8221 (tpt) REVERT: B 574 MET cc_start: 0.8104 (tpp) cc_final: 0.7752 (tpp) REVERT: B 669 LEU cc_start: 0.9358 (tp) cc_final: 0.9124 (tt) REVERT: C 221 ILE cc_start: 0.8926 (mm) cc_final: 0.8604 (mt) REVERT: C 404 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7911 (mt) REVERT: C 418 GLU cc_start: 0.8103 (tp30) cc_final: 0.7765 (tp30) REVERT: C 430 HIS cc_start: 0.7596 (t70) cc_final: 0.7075 (t70) REVERT: C 479 MET cc_start: 0.6231 (mpp) cc_final: 0.5994 (mpp) REVERT: C 521 TRP cc_start: 0.7397 (t60) cc_final: 0.6470 (t60) REVERT: C 574 MET cc_start: 0.8200 (tpp) cc_final: 0.7859 (tpp) REVERT: C 650 TYR cc_start: 0.6592 (m-80) cc_final: 0.6368 (m-80) REVERT: D 221 ILE cc_start: 0.8908 (mm) cc_final: 0.8574 (mt) REVERT: D 404 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7879 (mt) REVERT: D 418 GLU cc_start: 0.8095 (tp30) cc_final: 0.7752 (tp30) REVERT: D 430 HIS cc_start: 0.7597 (t70) cc_final: 0.7064 (t70) REVERT: D 449 PHE cc_start: 0.8174 (t80) cc_final: 0.7933 (t80) REVERT: D 479 MET cc_start: 0.6199 (mpp) cc_final: 0.5947 (mpp) REVERT: D 493 TRP cc_start: 0.8140 (t-100) cc_final: 0.7764 (t-100) REVERT: D 521 TRP cc_start: 0.7388 (t60) cc_final: 0.6451 (t60) REVERT: D 532 LEU cc_start: 0.8903 (tp) cc_final: 0.8567 (tp) REVERT: D 550 CYS cc_start: 0.8120 (m) cc_final: 0.7738 (t) REVERT: D 555 MET cc_start: 0.8698 (ptp) cc_final: 0.8451 (ptp) REVERT: D 574 MET cc_start: 0.8140 (tpp) cc_final: 0.7789 (tpp) outliers start: 69 outliers final: 10 residues processed: 368 average time/residue: 0.2990 time to fit residues: 175.8496 Evaluate side-chains 251 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 236 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 461 TYR 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: 2.9990 chunk 184 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 chunk 239 optimal weight: 2.9990 chunk 197 optimal weight: 0.5980 chunk 220 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 143 GLN B 197 ASN B 216 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN C 143 GLN C 197 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3566 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= 0.236 Angle : 0.647 13.034 27620 Z= 0.314 Chirality : 0.040 0.240 3152 Planarity : 0.004 0.041 3420 Dihedral : 6.403 49.216 2718 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.44 % Favored : 94.39 % Rotamer: Outliers : 3.24 % Allowed : 14.72 % Favored : 82.04 % 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: -1.78 (0.16), residues: 2408 helix: -0.14 (0.13), residues: 1476 sheet: -0.45 (0.46), residues: 92 loop : -3.17 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 493 HIS 0.006 0.001 HIS C 417 PHE 0.025 0.001 PHE A 489 TYR 0.019 0.001 TYR C 321 ARG 0.007 0.001 ARG A 696 *********************** 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 324 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 254 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 404 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8104 (mt) REVERT: A 418 GLU cc_start: 0.8161 (tp30) cc_final: 0.7877 (tp30) REVERT: A 430 HIS cc_start: 0.7701 (t70) cc_final: 0.7166 (t70) REVERT: A 479 MET cc_start: 0.6200 (mpp) cc_final: 0.5628 (mpp) REVERT: A 521 TRP cc_start: 0.7437 (t60) cc_final: 0.6495 (t60) REVERT: A 532 LEU cc_start: 0.9006 (tp) cc_final: 0.8702 (tp) REVERT: A 550 CYS cc_start: 0.8069 (m) cc_final: 0.7775 (t) REVERT: A 574 MET cc_start: 0.8181 (tpp) cc_final: 0.7856 (tpp) REVERT: A 578 MET cc_start: 0.8529 (tpp) cc_final: 0.8150 (tpp) REVERT: B 404 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8204 (mt) REVERT: B 418 GLU cc_start: 0.8084 (tp30) cc_final: 0.7793 (tp30) REVERT: B 449 PHE cc_start: 0.8147 (t80) cc_final: 0.7911 (t80) REVERT: B 461 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.7072 (t80) REVERT: B 532 LEU cc_start: 0.9002 (tp) cc_final: 0.8793 (tp) REVERT: B 550 CYS cc_start: 0.8135 (m) cc_final: 0.7891 (t) REVERT: B 574 MET cc_start: 0.8145 (tpp) cc_final: 0.7803 (tpp) REVERT: C 404 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8102 (mt) REVERT: C 418 GLU cc_start: 0.8144 (tp30) cc_final: 0.7868 (tp30) REVERT: C 479 MET cc_start: 0.6228 (mpp) cc_final: 0.5697 (mpp) REVERT: C 521 TRP cc_start: 0.7425 (t60) cc_final: 0.6490 (t60) REVERT: C 574 MET cc_start: 0.8226 (tpp) cc_final: 0.7897 (tpp) REVERT: C 578 MET cc_start: 0.8520 (tpp) cc_final: 0.8135 (tpp) REVERT: D 404 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8125 (mt) REVERT: D 418 GLU cc_start: 0.8146 (tp30) cc_final: 0.7858 (tp30) REVERT: D 430 HIS cc_start: 0.7703 (t70) cc_final: 0.7196 (t70) REVERT: D 449 PHE cc_start: 0.8160 (t80) cc_final: 0.7899 (t80) REVERT: D 461 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.6832 (t80) REVERT: D 479 MET cc_start: 0.6221 (mpp) cc_final: 0.5662 (mpp) REVERT: D 488 MET cc_start: 0.7485 (tpp) cc_final: 0.7225 (tpp) REVERT: D 521 TRP cc_start: 0.7436 (t60) cc_final: 0.6486 (t60) REVERT: D 532 LEU cc_start: 0.9011 (tp) cc_final: 0.8697 (tp) REVERT: D 550 CYS cc_start: 0.8077 (m) cc_final: 0.7753 (t) REVERT: D 574 MET cc_start: 0.8187 (tpp) cc_final: 0.7841 (tpp) outliers start: 70 outliers final: 27 residues processed: 301 average time/residue: 0.2693 time to fit residues: 133.7179 Evaluate side-chains 239 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain C residue 550 CYS Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 105 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 216 GLN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20424 Z= 0.279 Angle : 0.636 10.975 27620 Z= 0.315 Chirality : 0.041 0.212 3152 Planarity : 0.004 0.033 3420 Dihedral : 6.579 65.580 2718 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.32 % Favored : 94.52 % Rotamer: Outliers : 4.31 % Allowed : 14.58 % Favored : 81.11 % 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: -1.26 (0.16), residues: 2408 helix: 0.36 (0.13), residues: 1480 sheet: -0.31 (0.48), residues: 92 loop : -3.17 (0.18), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 493 HIS 0.007 0.001 HIS C 417 PHE 0.027 0.001 PHE B 489 TYR 0.018 0.001 TYR D 321 ARG 0.014 0.001 ARG A 696 *********************** 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 309 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 216 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASN cc_start: 0.7927 (p0) cc_final: 0.7712 (p0) REVERT: A 404 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8100 (mt) REVERT: A 479 MET cc_start: 0.6195 (mpp) cc_final: 0.5603 (mpp) REVERT: A 521 TRP cc_start: 0.7488 (t60) cc_final: 0.6499 (t60) REVERT: A 532 LEU cc_start: 0.9048 (tp) cc_final: 0.8761 (tp) REVERT: A 550 CYS cc_start: 0.8124 (m) cc_final: 0.7865 (t) REVERT: A 574 MET cc_start: 0.8222 (tpp) cc_final: 0.7907 (tpp) REVERT: A 578 MET cc_start: 0.8593 (tpp) cc_final: 0.8251 (tpp) REVERT: B 404 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8196 (mt) REVERT: B 449 PHE cc_start: 0.8216 (t80) cc_final: 0.7984 (t80) REVERT: B 521 TRP cc_start: 0.7402 (t60) cc_final: 0.6302 (t60) REVERT: B 532 LEU cc_start: 0.9055 (tp) cc_final: 0.8789 (tp) REVERT: B 550 CYS cc_start: 0.8145 (m) cc_final: 0.7932 (t) REVERT: B 574 MET cc_start: 0.8097 (tpp) cc_final: 0.7810 (tpp) REVERT: C 314 ASN cc_start: 0.7954 (p0) cc_final: 0.7739 (p0) REVERT: C 404 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8087 (mt) REVERT: C 418 GLU cc_start: 0.8281 (tp30) cc_final: 0.8074 (tp30) REVERT: C 479 MET cc_start: 0.6228 (mpp) cc_final: 0.5644 (mpp) REVERT: C 521 TRP cc_start: 0.7452 (t60) cc_final: 0.6381 (t60) REVERT: C 550 CYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8056 (t) REVERT: C 574 MET cc_start: 0.8197 (tpp) cc_final: 0.7903 (tpp) REVERT: C 578 MET cc_start: 0.8559 (tpp) cc_final: 0.8166 (tpp) REVERT: C 596 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8402 (mm) REVERT: D 314 ASN cc_start: 0.7984 (p0) cc_final: 0.7768 (p0) REVERT: D 404 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8204 (mt) REVERT: D 449 PHE cc_start: 0.8241 (t80) cc_final: 0.7941 (t80) REVERT: D 479 MET cc_start: 0.6270 (mpp) cc_final: 0.5667 (mpp) REVERT: D 521 TRP cc_start: 0.7453 (t60) cc_final: 0.6427 (t60) REVERT: D 532 LEU cc_start: 0.9040 (tp) cc_final: 0.8761 (tp) REVERT: D 550 CYS cc_start: 0.8137 (m) cc_final: 0.7850 (t) REVERT: D 574 MET cc_start: 0.8210 (tpp) cc_final: 0.7876 (tpp) outliers start: 93 outliers final: 32 residues processed: 283 average time/residue: 0.2697 time to fit residues: 125.4419 Evaluate side-chains 236 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 198 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 550 CYS Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 436 PHE Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4225 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= 0.197 Angle : 0.592 10.510 27620 Z= 0.289 Chirality : 0.039 0.185 3152 Planarity : 0.003 0.029 3420 Dihedral : 6.214 65.496 2716 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.57 % Favored : 95.27 % Rotamer: Outliers : 3.43 % Allowed : 15.23 % Favored : 81.34 % 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: -0.94 (0.17), residues: 2408 helix: 0.59 (0.13), residues: 1492 sheet: -0.16 (0.48), residues: 92 loop : -3.05 (0.18), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 493 HIS 0.004 0.001 HIS C 417 PHE 0.025 0.001 PHE A 590 TYR 0.015 0.001 TYR C 321 ARG 0.003 0.000 ARG A 147 *********************** 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 300 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 226 time to evaluate : 2.461 Fit side-chains revert: symmetry clash REVERT: A 404 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8095 (mt) REVERT: A 521 TRP cc_start: 0.7389 (t60) cc_final: 0.6345 (t60) REVERT: A 532 LEU cc_start: 0.9034 (tp) cc_final: 0.8759 (tp) REVERT: A 574 MET cc_start: 0.8164 (tpp) cc_final: 0.7869 (tpp) REVERT: A 578 MET cc_start: 0.8628 (tpp) cc_final: 0.8292 (tpt) REVERT: B 419 MET cc_start: 0.8497 (mtp) cc_final: 0.8280 (ttm) REVERT: B 449 PHE cc_start: 0.8184 (t80) cc_final: 0.7927 (t80) REVERT: B 521 TRP cc_start: 0.7315 (t60) cc_final: 0.6222 (t60) REVERT: B 532 LEU cc_start: 0.9036 (tp) cc_final: 0.8777 (tp) REVERT: B 574 MET cc_start: 0.8014 (tpp) cc_final: 0.7802 (tpp) REVERT: C 404 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8133 (mt) REVERT: C 418 GLU cc_start: 0.8189 (tp30) cc_final: 0.7928 (tp30) REVERT: C 479 MET cc_start: 0.6220 (mpp) cc_final: 0.5630 (mpp) REVERT: C 521 TRP cc_start: 0.7429 (t60) cc_final: 0.6899 (t60) REVERT: C 550 CYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8234 (t) REVERT: C 574 MET cc_start: 0.8109 (tpp) cc_final: 0.7874 (tpp) REVERT: C 578 MET cc_start: 0.8639 (tpp) cc_final: 0.8253 (tpt) REVERT: C 596 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8384 (mm) REVERT: C 672 MET cc_start: 0.8906 (ttp) cc_final: 0.8597 (ttp) REVERT: C 731 CYS cc_start: 0.8666 (m) cc_final: 0.8006 (m) REVERT: D 404 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8114 (mt) REVERT: D 449 PHE cc_start: 0.8188 (t80) cc_final: 0.7869 (t80) REVERT: D 521 TRP cc_start: 0.7438 (t60) cc_final: 0.6411 (t60) REVERT: D 532 LEU cc_start: 0.9033 (tp) cc_final: 0.8740 (tp) REVERT: D 550 CYS cc_start: 0.8055 (m) cc_final: 0.7853 (t) REVERT: D 574 MET cc_start: 0.8132 (tpp) cc_final: 0.7842 (tpp) REVERT: D 672 MET cc_start: 0.8926 (ttp) cc_final: 0.8567 (ttp) outliers start: 74 outliers final: 34 residues processed: 275 average time/residue: 0.2744 time to fit residues: 125.7877 Evaluate side-chains 234 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 195 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 550 CYS Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 236 optimal weight: 7.9990 chunk 195 optimal weight: 0.0870 chunk 109 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 529 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20424 Z= 0.173 Angle : 0.628 15.593 27620 Z= 0.293 Chirality : 0.039 0.246 3152 Planarity : 0.003 0.027 3420 Dihedral : 5.959 63.388 2714 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 3.10 % Allowed : 15.83 % Favored : 81.06 % 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: -0.76 (0.17), residues: 2408 helix: 0.73 (0.14), residues: 1484 sheet: -0.14 (0.49), residues: 92 loop : -2.92 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 710 HIS 0.004 0.001 HIS A 417 PHE 0.020 0.001 PHE A 590 TYR 0.019 0.001 TYR D 661 ARG 0.002 0.000 ARG A 147 *********************** 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 280 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 213 time to evaluate : 2.448 Fit side-chains revert: symmetry clash REVERT: A 404 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8163 (mt) REVERT: A 521 TRP cc_start: 0.7377 (t60) cc_final: 0.6349 (t60) REVERT: A 532 LEU cc_start: 0.9191 (tp) cc_final: 0.8961 (tp) REVERT: A 562 MET cc_start: 0.8384 (mmm) cc_final: 0.8139 (mmm) REVERT: A 574 MET cc_start: 0.8173 (tpp) cc_final: 0.7900 (tpp) REVERT: A 578 MET cc_start: 0.8682 (tpp) cc_final: 0.8355 (tpt) REVERT: A 731 CYS cc_start: 0.8656 (m) cc_final: 0.8109 (m) REVERT: B 449 PHE cc_start: 0.8190 (t80) cc_final: 0.7947 (t80) REVERT: B 521 TRP cc_start: 0.7267 (t60) cc_final: 0.6128 (t60) REVERT: B 532 LEU cc_start: 0.9158 (tp) cc_final: 0.8957 (tp) REVERT: B 672 MET cc_start: 0.8867 (ttp) cc_final: 0.8371 (ttp) REVERT: B 731 CYS cc_start: 0.8662 (m) cc_final: 0.8131 (m) REVERT: C 521 TRP cc_start: 0.7390 (t60) cc_final: 0.6412 (t60) REVERT: C 561 ASN cc_start: 0.8908 (m-40) cc_final: 0.8677 (t0) REVERT: C 574 MET cc_start: 0.8130 (tpp) cc_final: 0.7909 (tpp) REVERT: C 672 MET cc_start: 0.8839 (ttp) cc_final: 0.8401 (ttp) REVERT: C 731 CYS cc_start: 0.8681 (m) cc_final: 0.8043 (m) REVERT: C 738 LYS cc_start: 0.8581 (mttt) cc_final: 0.8330 (pttm) REVERT: D 404 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8199 (mt) REVERT: D 449 PHE cc_start: 0.8169 (t80) cc_final: 0.7836 (t80) REVERT: D 521 TRP cc_start: 0.7364 (t60) cc_final: 0.6327 (t60) REVERT: D 532 LEU cc_start: 0.9049 (tp) cc_final: 0.8734 (tp) REVERT: D 574 MET cc_start: 0.8162 (tpp) cc_final: 0.7897 (tpp) REVERT: D 672 MET cc_start: 0.8861 (ttp) cc_final: 0.8504 (ttp) REVERT: D 731 CYS cc_start: 0.8649 (m) cc_final: 0.8111 (m) outliers start: 67 outliers final: 31 residues processed: 258 average time/residue: 0.2608 time to fit residues: 112.8345 Evaluate side-chains 232 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 199 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 550 CYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 694 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 6.9990 chunk 26 optimal weight: 0.0270 chunk 134 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 198 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 235 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 108 optimal weight: 30.0000 overall best weight: 2.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN C 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4604 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= 0.218 Angle : 0.645 15.072 27620 Z= 0.302 Chirality : 0.040 0.250 3152 Planarity : 0.003 0.028 3420 Dihedral : 6.027 63.161 2712 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.48 % Favored : 94.39 % Rotamer: Outliers : 2.82 % Allowed : 16.57 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.79 (0.17), residues: 2408 helix: 0.74 (0.14), residues: 1488 sheet: -0.09 (0.50), residues: 92 loop : -3.03 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 710 HIS 0.006 0.001 HIS D 417 PHE 0.015 0.001 PHE A 715 TYR 0.014 0.001 TYR B 661 ARG 0.004 0.000 ARG D 714 *********************** 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 276 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 215 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8197 (mt) REVERT: A 521 TRP cc_start: 0.7361 (t60) cc_final: 0.6371 (t60) REVERT: A 532 LEU cc_start: 0.9190 (tp) cc_final: 0.8978 (tp) REVERT: A 574 MET cc_start: 0.8217 (tpp) cc_final: 0.8001 (tpp) REVERT: A 578 MET cc_start: 0.8639 (tpp) cc_final: 0.8270 (tpt) REVERT: A 731 CYS cc_start: 0.8615 (m) cc_final: 0.8024 (m) REVERT: B 449 PHE cc_start: 0.8203 (t80) cc_final: 0.7949 (t80) REVERT: B 521 TRP cc_start: 0.7271 (t60) cc_final: 0.6234 (t60) REVERT: B 532 LEU cc_start: 0.9142 (tp) cc_final: 0.8919 (tp) REVERT: B 731 CYS cc_start: 0.8700 (m) cc_final: 0.8154 (m) REVERT: C 521 TRP cc_start: 0.7352 (t60) cc_final: 0.6376 (t60) REVERT: C 561 ASN cc_start: 0.8941 (m-40) cc_final: 0.8728 (t0) REVERT: C 578 MET cc_start: 0.8654 (tpp) cc_final: 0.8283 (tpt) REVERT: C 731 CYS cc_start: 0.8709 (m) cc_final: 0.8117 (m) REVERT: C 738 LYS cc_start: 0.8609 (mttt) cc_final: 0.8357 (pttm) REVERT: D 404 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8205 (mt) REVERT: D 449 PHE cc_start: 0.8206 (t80) cc_final: 0.7905 (t80) REVERT: D 461 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.7229 (t80) REVERT: D 521 TRP cc_start: 0.7356 (t60) cc_final: 0.6359 (t60) REVERT: D 532 LEU cc_start: 0.9204 (tp) cc_final: 0.8948 (tp) REVERT: D 672 MET cc_start: 0.8902 (ttp) cc_final: 0.8431 (ttp) REVERT: D 731 CYS cc_start: 0.8608 (m) cc_final: 0.8033 (m) outliers start: 61 outliers final: 41 residues processed: 252 average time/residue: 0.2717 time to fit residues: 112.9677 Evaluate side-chains 242 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 550 CYS Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 HIS B 452 ASN C 244 HIS C 452 ASN D 244 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20424 Z= 0.153 Angle : 0.625 13.412 27620 Z= 0.291 Chirality : 0.038 0.236 3152 Planarity : 0.003 0.027 3420 Dihedral : 5.767 62.229 2712 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.36 % Favored : 95.47 % Rotamer: Outliers : 2.08 % Allowed : 17.69 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.17), residues: 2408 helix: 0.91 (0.14), residues: 1460 sheet: -0.11 (0.49), residues: 92 loop : -2.70 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 710 HIS 0.003 0.001 HIS C 426 PHE 0.021 0.001 PHE A 715 TYR 0.013 0.001 TYR B 661 ARG 0.002 0.000 ARG C 371 *********************** 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 277 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 232 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 TRP cc_start: 0.7329 (t60) cc_final: 0.6365 (t60) REVERT: A 532 LEU cc_start: 0.9149 (tp) cc_final: 0.8937 (tp) REVERT: A 731 CYS cc_start: 0.8519 (m) cc_final: 0.7920 (m) REVERT: B 159 MET cc_start: 0.8958 (mmp) cc_final: 0.8726 (mmp) REVERT: B 449 PHE cc_start: 0.8138 (t80) cc_final: 0.7877 (t80) REVERT: B 521 TRP cc_start: 0.7228 (t60) cc_final: 0.6184 (t60) REVERT: B 532 LEU cc_start: 0.9139 (tp) cc_final: 0.8904 (tp) REVERT: B 672 MET cc_start: 0.8749 (ttp) cc_final: 0.8160 (ttm) REVERT: B 717 MET cc_start: 0.7266 (tpt) cc_final: 0.7034 (tpp) REVERT: B 731 CYS cc_start: 0.8629 (m) cc_final: 0.8085 (m) REVERT: C 521 TRP cc_start: 0.7314 (t60) cc_final: 0.6766 (t60) REVERT: C 578 MET cc_start: 0.8631 (tpp) cc_final: 0.8363 (tpt) REVERT: C 672 MET cc_start: 0.8857 (ttp) cc_final: 0.8305 (ttm) REVERT: C 731 CYS cc_start: 0.8675 (m) cc_final: 0.8047 (m) REVERT: C 738 LYS cc_start: 0.8599 (mttt) cc_final: 0.8323 (pttm) REVERT: D 449 PHE cc_start: 0.8144 (t80) cc_final: 0.7815 (t80) REVERT: D 521 TRP cc_start: 0.7338 (t60) cc_final: 0.6393 (t60) REVERT: D 532 LEU cc_start: 0.9135 (tp) cc_final: 0.8927 (tp) REVERT: D 672 MET cc_start: 0.8847 (ttp) cc_final: 0.8473 (ttp) REVERT: D 731 CYS cc_start: 0.8528 (m) cc_final: 0.7930 (m) outliers start: 45 outliers final: 31 residues processed: 255 average time/residue: 0.2909 time to fit residues: 119.0331 Evaluate side-chains 235 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 436 PHE Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 7.9990 chunk 225 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 67 optimal weight: 0.3980 chunk 198 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 452 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN C 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4875 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= 0.186 Angle : 0.639 13.928 27620 Z= 0.298 Chirality : 0.039 0.225 3152 Planarity : 0.003 0.029 3420 Dihedral : 5.700 61.175 2708 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.19 % Favored : 94.64 % Rotamer: Outliers : 1.94 % Allowed : 18.15 % Favored : 79.91 % 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: -0.58 (0.17), residues: 2408 helix: 0.87 (0.14), residues: 1460 sheet: -0.14 (0.50), residues: 92 loop : -2.73 (0.18), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 710 HIS 0.004 0.001 HIS C 417 PHE 0.022 0.001 PHE A 715 TYR 0.022 0.001 TYR C 451 ARG 0.003 0.000 ARG D 696 *********************** 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 257 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 215 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 TRP cc_start: 0.7365 (t60) cc_final: 0.6420 (t60) REVERT: A 532 LEU cc_start: 0.9153 (tp) cc_final: 0.8942 (tp) REVERT: A 731 CYS cc_start: 0.8539 (m) cc_final: 0.7926 (m) REVERT: B 449 PHE cc_start: 0.8161 (t80) cc_final: 0.7922 (t80) REVERT: B 521 TRP cc_start: 0.7237 (t60) cc_final: 0.6194 (t60) REVERT: B 532 LEU cc_start: 0.9145 (tp) cc_final: 0.8910 (tp) REVERT: B 672 MET cc_start: 0.8799 (ttp) cc_final: 0.8482 (ttp) REVERT: B 731 CYS cc_start: 0.8651 (m) cc_final: 0.8113 (m) REVERT: C 521 TRP cc_start: 0.7293 (t60) cc_final: 0.6364 (t60) REVERT: C 561 ASN cc_start: 0.8903 (t0) cc_final: 0.8529 (t0) REVERT: C 578 MET cc_start: 0.8656 (tpp) cc_final: 0.8387 (tpt) REVERT: C 672 MET cc_start: 0.8848 (ttp) cc_final: 0.8560 (ttp) REVERT: C 731 CYS cc_start: 0.8690 (m) cc_final: 0.8101 (m) REVERT: C 738 LYS cc_start: 0.8585 (mttt) cc_final: 0.8318 (pttm) REVERT: D 159 MET cc_start: 0.8879 (mmm) cc_final: 0.8664 (mmp) REVERT: D 449 PHE cc_start: 0.8158 (t80) cc_final: 0.7836 (t80) REVERT: D 521 TRP cc_start: 0.7369 (t60) cc_final: 0.6425 (t60) REVERT: D 532 LEU cc_start: 0.9143 (tp) cc_final: 0.8936 (tp) REVERT: D 672 MET cc_start: 0.8851 (ttp) cc_final: 0.8514 (ttp) REVERT: D 731 CYS cc_start: 0.8549 (m) cc_final: 0.7935 (m) outliers start: 42 outliers final: 32 residues processed: 237 average time/residue: 0.2841 time to fit residues: 108.8942 Evaluate side-chains 236 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 204 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 chunk 141 optimal weight: 0.2980 chunk 109 optimal weight: 4.9990 chunk 161 optimal weight: 0.0050 chunk 243 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20424 Z= 0.151 Angle : 0.630 13.598 27620 Z= 0.293 Chirality : 0.039 0.272 3152 Planarity : 0.003 0.026 3420 Dihedral : 5.546 60.216 2708 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.24 % Favored : 95.60 % Rotamer: Outliers : 1.25 % Allowed : 18.84 % Favored : 79.91 % 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: -0.53 (0.17), residues: 2408 helix: 0.92 (0.14), residues: 1468 sheet: -0.13 (0.50), residues: 92 loop : -2.77 (0.18), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 710 HIS 0.003 0.001 HIS D 426 PHE 0.026 0.001 PHE D 656 TYR 0.021 0.001 TYR A 321 ARG 0.003 0.000 ARG D 696 ********************** 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 243 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 216 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 TRP cc_start: 0.7319 (t60) cc_final: 0.6360 (t60) REVERT: A 532 LEU cc_start: 0.9137 (tp) cc_final: 0.8928 (tp) REVERT: A 731 CYS cc_start: 0.8502 (m) cc_final: 0.7913 (m) REVERT: B 449 PHE cc_start: 0.8128 (t80) cc_final: 0.7872 (t80) REVERT: B 479 MET cc_start: 0.6121 (mpp) cc_final: 0.5613 (mpp) REVERT: B 521 TRP cc_start: 0.7226 (t60) cc_final: 0.6180 (t60) REVERT: B 532 LEU cc_start: 0.9133 (tp) cc_final: 0.8903 (tp) REVERT: B 672 MET cc_start: 0.8781 (ttp) cc_final: 0.8474 (ttp) REVERT: B 731 CYS cc_start: 0.8560 (m) cc_final: 0.7980 (m) REVERT: C 334 GLU cc_start: 0.7885 (tt0) cc_final: 0.7498 (tt0) REVERT: C 521 TRP cc_start: 0.7278 (t60) cc_final: 0.6342 (t60) REVERT: C 561 ASN cc_start: 0.8823 (t0) cc_final: 0.8451 (t0) REVERT: C 578 MET cc_start: 0.8639 (tpp) cc_final: 0.8364 (tpt) REVERT: C 672 MET cc_start: 0.8803 (ttp) cc_final: 0.8309 (ttm) REVERT: C 731 CYS cc_start: 0.8663 (m) cc_final: 0.8087 (m) REVERT: C 738 LYS cc_start: 0.8586 (mttt) cc_final: 0.8294 (pttm) REVERT: D 159 MET cc_start: 0.8835 (mmm) cc_final: 0.8613 (mmp) REVERT: D 449 PHE cc_start: 0.8139 (t80) cc_final: 0.7834 (t80) REVERT: D 521 TRP cc_start: 0.7345 (t60) cc_final: 0.6400 (t60) REVERT: D 532 LEU cc_start: 0.9119 (tp) cc_final: 0.8917 (tp) REVERT: D 672 MET cc_start: 0.8832 (ttp) cc_final: 0.8485 (ttp) REVERT: D 731 CYS cc_start: 0.8487 (m) cc_final: 0.7906 (m) outliers start: 27 outliers final: 25 residues processed: 229 average time/residue: 0.2839 time to fit residues: 104.9086 Evaluate side-chains 231 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 206 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 178 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN C 529 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.146029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.106439 restraints weight = 41215.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.110087 restraints weight = 21406.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.112406 restraints weight = 14454.281| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20424 Z= 0.134 Angle : 0.625 13.443 27620 Z= 0.288 Chirality : 0.038 0.271 3152 Planarity : 0.003 0.026 3420 Dihedral : 5.277 55.946 2708 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.28 % Favored : 95.60 % Rotamer: Outliers : 1.34 % Allowed : 18.89 % Favored : 79.77 % 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: -0.44 (0.17), residues: 2408 helix: 0.91 (0.14), residues: 1484 sheet: 0.34 (0.51), residues: 88 loop : -2.67 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 710 HIS 0.003 0.001 HIS C 426 PHE 0.026 0.001 PHE D 656 TYR 0.029 0.001 TYR C 451 ARG 0.003 0.000 ARG D 696 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3767.02 seconds wall clock time: 69 minutes 55.53 seconds (4195.53 seconds total)