Starting phenix.real_space_refine on Fri Aug 7 10:40:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13lr_77142/08_2026/13lr_77142.cif Found real_map, /net/cci-nas-00/data/ceres_data/13lr_77142/08_2026/13lr_77142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13lr_77142/08_2026/13lr_77142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13lr_77142/08_2026/13lr_77142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13lr_77142/08_2026/13lr_77142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13lr_77142/08_2026/13lr_77142.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.027 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 124 5.16 5 Na 3 4.78 5 C 13500 2.51 5 N 3296 2.21 5 O 3640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20575 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4987 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 14, 'TRANS': 597} Chain breaks: 2 Chain: "B" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4987 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 14, 'TRANS': 597} Chain breaks: 2 Chain: "C" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4987 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 14, 'TRANS': 597} Chain breaks: 2 Chain: "D" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4987 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 14, 'TRANS': 597} Chain breaks: 2 Chain: "A" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 211 Unusual residues: {' NA': 3, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.99, per 1000 atoms: 0.24 Number of scatterers: 20575 At special positions: 0 Unit cell: (155.979, 156.96, 132.435, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 12 15.00 Na 3 11.00 O 3640 8.00 N 3296 7.00 C 13500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 890.7 milliseconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 8 sheets defined 59.8% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.725A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 147 removed outlier: 3.870A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.554A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.586A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.788A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.647A pdb=" N ALA A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.666A pdb=" N LEU A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.743A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.675A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.648A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.521A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.537A pdb=" N THR A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.665A pdb=" N LEU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 431 through 436 removed outlier: 3.611A pdb=" N LYS A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 431 through 436' Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 448 through 461 removed outlier: 3.740A pdb=" N THR A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 508 removed outlier: 3.542A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 497 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 539 removed outlier: 3.577A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 559 removed outlier: 3.835A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 569 removed outlier: 3.663A pdb=" N TYR A 565 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE A 569 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 3.821A pdb=" N SER A 576 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 removed outlier: 3.960A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.522A pdb=" N ALA A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 679 removed outlier: 3.825A pdb=" N PHE A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 685 through 707 removed outlier: 3.545A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.725A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 147 removed outlier: 3.871A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.555A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.585A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.788A pdb=" N ASN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.647A pdb=" N ALA B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.666A pdb=" N LEU B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.743A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.676A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.647A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.520A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.536A pdb=" N THR B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.665A pdb=" N LEU B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 431 through 436 removed outlier: 3.611A pdb=" N LYS B 435 " --> pdb=" O MET B 431 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 431 through 436' Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 448 through 461 removed outlier: 3.738A pdb=" N THR B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 508 removed outlier: 3.542A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N MET B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 497 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 539 removed outlier: 3.578A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 559 removed outlier: 3.836A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 removed outlier: 3.663A pdb=" N TYR B 565 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE B 569 " --> pdb=" O THR B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 3.819A pdb=" N SER B 576 " --> pdb=" O MET B 572 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 608 removed outlier: 3.961A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 removed outlier: 3.522A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 679 removed outlier: 3.825A pdb=" N PHE B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 684 Processing helix chain 'B' and resid 685 through 707 removed outlier: 3.545A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.725A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 147 removed outlier: 3.869A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.555A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.586A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.789A pdb=" N ASN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.647A pdb=" N ALA C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.666A pdb=" N LEU C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.744A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.668A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.647A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 removed outlier: 3.520A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.536A pdb=" N THR C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.665A pdb=" N LEU C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 431 through 436 removed outlier: 3.611A pdb=" N LYS C 435 " --> pdb=" O MET C 431 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 431 through 436' Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 448 through 461 removed outlier: 3.740A pdb=" N THR C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 508 removed outlier: 3.542A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N MET C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 497 " --> pdb=" O TRP C 493 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER C 498 " --> pdb=" O ALA C 494 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 539 removed outlier: 3.578A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 559 removed outlier: 3.836A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 569 removed outlier: 3.663A pdb=" N TYR C 565 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE C 569 " --> pdb=" O THR C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 578 removed outlier: 3.820A pdb=" N SER C 576 " --> pdb=" O MET C 572 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 608 removed outlier: 3.960A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 3.522A pdb=" N ALA C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 632 " --> pdb=" O ALA C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 679 removed outlier: 3.825A pdb=" N PHE C 654 " --> pdb=" O TYR C 650 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 684 Processing helix chain 'C' and resid 685 through 707 removed outlier: 3.545A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.726A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 147 removed outlier: 3.870A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 158 Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.555A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.585A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.788A pdb=" N ASN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.647A pdb=" N ALA D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.666A pdb=" N LEU D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.743A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.678A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.647A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.520A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 3.537A pdb=" N THR D 407 " --> pdb=" O VAL D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.665A pdb=" N LEU D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 431 through 436 removed outlier: 3.612A pdb=" N LYS D 435 " --> pdb=" O MET D 431 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 431 through 436' Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 448 through 461 removed outlier: 3.738A pdb=" N THR D 456 " --> pdb=" O ASN D 452 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 457 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 508 removed outlier: 3.542A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA D 494 " --> pdb=" O VAL D 490 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 497 " --> pdb=" O TRP D 493 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 539 removed outlier: 3.577A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 559 removed outlier: 3.836A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 569 removed outlier: 3.663A pdb=" N TYR D 565 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE D 569 " --> pdb=" O THR D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 578 removed outlier: 3.819A pdb=" N SER D 576 " --> pdb=" O MET D 572 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 608 removed outlier: 3.961A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 removed outlier: 3.522A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 632 " --> pdb=" O ALA D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 679 removed outlier: 3.825A pdb=" N PHE D 654 " --> pdb=" O TYR D 650 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 684 Processing helix chain 'D' and resid 685 through 707 removed outlier: 3.545A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 380 through 381 removed outlier: 3.606A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AA3, first strand: chain 'B' and resid 380 through 381 removed outlier: 3.607A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 719 through 722 Processing sheet with id=AA5, first strand: chain 'C' and resid 380 through 381 removed outlier: 3.606A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 719 through 722 Processing sheet with id=AA7, first strand: chain 'D' and resid 380 through 381 removed outlier: 3.606A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 719 through 722 761 hydrogen bonds defined for protein. 2211 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: 2.14 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3515 1.32 - 1.44: 5328 1.44 - 1.57: 11925 1.57 - 1.69: 24 1.69 - 1.81: 204 Bond restraints: 20996 Sorted by residual: bond pdb=" C VAL D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 1.337 1.385 -0.048 1.11e-02 8.12e+03 1.88e+01 bond pdb=" C VAL C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.337 1.385 -0.048 1.11e-02 8.12e+03 1.88e+01 bond pdb=" C VAL A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.337 1.385 -0.048 1.11e-02 8.12e+03 1.88e+01 bond pdb=" C VAL B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.337 1.384 -0.047 1.11e-02 8.12e+03 1.80e+01 bond pdb=" N VAL C 684 " pdb=" CA VAL C 684 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.09e+01 ... (remaining 20991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 26436 2.13 - 4.25: 1617 4.25 - 6.38: 159 6.38 - 8.50: 52 8.50 - 10.63: 16 Bond angle restraints: 28280 Sorted by residual: angle pdb=" C ASP B 586 " pdb=" N VAL B 587 " pdb=" CA VAL B 587 " ideal model delta sigma weight residual 121.97 132.60 -10.63 1.80e+00 3.09e-01 3.49e+01 angle pdb=" C ASP A 586 " pdb=" N VAL A 587 " pdb=" CA VAL A 587 " ideal model delta sigma weight residual 121.97 132.57 -10.60 1.80e+00 3.09e-01 3.47e+01 angle pdb=" C ASP D 586 " pdb=" N VAL D 587 " pdb=" CA VAL D 587 " ideal model delta sigma weight residual 121.97 132.57 -10.60 1.80e+00 3.09e-01 3.47e+01 angle pdb=" C ASP C 586 " pdb=" N VAL C 587 " pdb=" CA VAL C 587 " ideal model delta sigma weight residual 121.97 132.54 -10.57 1.80e+00 3.09e-01 3.45e+01 angle pdb=" C ASN B 616 " pdb=" N LYS B 617 " pdb=" CA LYS B 617 " ideal model delta sigma weight residual 122.08 129.38 -7.30 1.47e+00 4.63e-01 2.46e+01 ... (remaining 28275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 12403 35.96 - 71.92: 205 71.92 - 107.88: 19 107.88 - 143.84: 13 143.84 - 179.81: 12 Dihedral angle restraints: 12652 sinusoidal: 5444 harmonic: 7208 Sorted by residual: dihedral pdb=" CA ASP B 586 " pdb=" C ASP B 586 " pdb=" N VAL B 587 " pdb=" CA VAL B 587 " ideal model delta harmonic sigma weight residual -180.00 -154.52 -25.48 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ASP A 586 " pdb=" C ASP A 586 " pdb=" N VAL A 587 " pdb=" CA VAL A 587 " ideal model delta harmonic sigma weight residual -180.00 -154.53 -25.47 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ASP D 586 " pdb=" C ASP D 586 " pdb=" N VAL D 587 " pdb=" CA VAL D 587 " ideal model delta harmonic sigma weight residual 180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 12649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2420 0.053 - 0.106: 596 0.106 - 0.159: 107 0.159 - 0.213: 17 0.213 - 0.266: 12 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CG LEU C 676 " pdb=" CB LEU C 676 " pdb=" CD1 LEU C 676 " pdb=" CD2 LEU C 676 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CG LEU D 676 " pdb=" CB LEU D 676 " pdb=" CD1 LEU D 676 " pdb=" CD2 LEU D 676 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CG LEU A 676 " pdb=" CB LEU A 676 " pdb=" CD1 LEU A 676 " pdb=" CD2 LEU A 676 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3149 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 314 " 0.014 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C ASN C 314 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN C 314 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP C 315 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 180 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.92e+00 pdb=" N PRO B 181 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 180 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO A 181 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.039 5.00e-02 4.00e+02 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6117 2.81 - 3.33: 17837 3.33 - 3.86: 31088 3.86 - 4.38: 37545 4.38 - 4.90: 63976 Nonbonded interactions: 156563 Sorted by model distance: nonbonded pdb=" OG1 THR C 399 " pdb=" O ASN C 401 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR B 399 " pdb=" O ASN B 401 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR A 399 " pdb=" O ASN A 401 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR D 399 " pdb=" O ASN D 401 " model vdw 2.292 3.040 nonbonded pdb=" OD1 ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.305 3.040 ... (remaining 156558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 118 through 1102) selection = chain 'B' selection = (chain 'C' and resid 118 through 1102) selection = (chain 'D' and resid 118 through 1102) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.950 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.008 0.072 21000 Z= 0.367 Angle : 1.141 10.630 28288 Z= 0.671 Chirality : 0.051 0.266 3152 Planarity : 0.006 0.070 3468 Dihedral : 15.646 179.806 7960 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.26 % Favored : 91.91 % Rotamer: Outliers : 0.37 % Allowed : 6.55 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.32 (0.10), residues: 2424 helix: -4.68 (0.05), residues: 1488 sheet: -4.27 (0.37), residues: 96 loop : -2.68 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 226 TYR 0.026 0.002 TYR A 409 PHE 0.024 0.002 PHE B 259 TRP 0.022 0.003 TRP B 692 HIS 0.008 0.002 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00812 / 0.37 (20996) covalent geometry : angle 1.14060 / 0.67 (28280) SS BOND : bond 0.00095 / 0.05 ( 4) SS BOND : angle 0.82864 / 0.53 ( 8) hydrogen bonds : bond 0.34408 / 22.64 ( 761) hydrogen bonds : angle 10.13048 / 6.94 ( 2211) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 363 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8274 (mmtt) cc_final: 0.7957 (ttmm) REVERT: A 323 MET cc_start: 0.8404 (ttm) cc_final: 0.8098 (ttm) REVERT: A 481 TRP cc_start: 0.5031 (m-90) cc_final: 0.4562 (m100) REVERT: A 484 LEU cc_start: 0.7790 (mm) cc_final: 0.6620 (tp) REVERT: A 671 ASN cc_start: 0.7898 (t160) cc_final: 0.7252 (t0) REVERT: B 161 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7971 (ttmm) REVERT: B 217 THR cc_start: 0.9165 (p) cc_final: 0.8950 (t) REVERT: B 323 MET cc_start: 0.8383 (ttm) cc_final: 0.8061 (ttm) REVERT: B 481 TRP cc_start: 0.5000 (m-90) cc_final: 0.4546 (m100) REVERT: B 484 LEU cc_start: 0.7819 (mm) cc_final: 0.6633 (tp) REVERT: B 671 ASN cc_start: 0.7894 (t160) cc_final: 0.7501 (t0) REVERT: C 161 LYS cc_start: 0.8313 (mmtt) cc_final: 0.7938 (ttmm) REVERT: C 323 MET cc_start: 0.8448 (ttm) cc_final: 0.8197 (ttm) REVERT: C 481 TRP cc_start: 0.5013 (m-90) cc_final: 0.4570 (m100) REVERT: C 484 LEU cc_start: 0.7818 (mm) cc_final: 0.6641 (tp) REVERT: D 161 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7966 (ttmm) REVERT: D 217 THR cc_start: 0.9165 (p) cc_final: 0.8946 (t) REVERT: D 323 MET cc_start: 0.8393 (ttm) cc_final: 0.8072 (ttm) REVERT: D 481 TRP cc_start: 0.5067 (m-90) cc_final: 0.4593 (m100) REVERT: D 484 LEU cc_start: 0.7794 (mm) cc_final: 0.6602 (tp) REVERT: D 671 ASN cc_start: 0.7924 (t160) cc_final: 0.7549 (t0) outliers start: 8 outliers final: 0 residues processed: 371 average time/residue: 0.1402 time to fit residues: 80.2486 Evaluate side-chains 207 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN A 220 ASN A 410 ASN A 647 ASN A 735 ASN A 750 ASN B 197 ASN B 220 ASN B 410 ASN B 647 ASN B 735 ASN B 750 ASN C 197 ASN C 220 ASN C 410 ASN C 647 ASN C 735 ASN C 750 ASN D 197 ASN D 220 ASN D 410 ASN D 647 ASN D 735 ASN D 750 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.148013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.096418 restraints weight = 33577.225| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.93 r_work: 0.3126 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21000 Z= 0.155 Angle : 0.664 8.194 28288 Z= 0.351 Chirality : 0.039 0.129 3152 Planarity : 0.005 0.046 3468 Dihedral : 17.533 172.757 3168 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.01 % Favored : 92.66 % Rotamer: Outliers : 1.61 % Allowed : 9.18 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.13), residues: 2424 helix: -2.78 (0.10), residues: 1524 sheet: -3.05 (0.50), residues: 88 loop : -3.04 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 188 TYR 0.022 0.002 TYR C 661 PHE 0.021 0.002 PHE D 590 TRP 0.018 0.002 TRP B 493 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (20996) covalent geometry : angle 0.66394 / 0.35 (28280) SS BOND : bond 0.00248 / 0.12 ( 4) SS BOND : angle 0.60096 / 0.39 ( 8) hydrogen bonds : bond 0.04600 / 3.08 ( 761) hydrogen bonds : angle 4.62569 / 3.19 ( 2211) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7511 (ttmm) REVERT: A 332 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7975 (mt-10) REVERT: A 488 MET cc_start: 0.7749 (mpm) cc_final: 0.7350 (mpp) REVERT: A 661 TYR cc_start: 0.7583 (t80) cc_final: 0.7333 (t80) REVERT: A 671 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7537 (m-40) REVERT: A 686 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7513 (pttp) REVERT: B 161 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7543 (ttmm) REVERT: B 332 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7991 (mt-10) REVERT: B 488 MET cc_start: 0.7742 (mpm) cc_final: 0.7352 (mpp) REVERT: B 661 TYR cc_start: 0.7594 (t80) cc_final: 0.7290 (t80) REVERT: B 671 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7518 (t0) REVERT: B 686 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7384 (pttp) REVERT: C 141 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8664 (tm-30) REVERT: C 161 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7470 (ttmm) REVERT: C 488 MET cc_start: 0.7769 (mpm) cc_final: 0.7396 (mpp) REVERT: C 661 TYR cc_start: 0.7596 (t80) cc_final: 0.7366 (t80) REVERT: C 671 ASN cc_start: 0.7901 (t0) cc_final: 0.7254 (t0) REVERT: D 161 LYS cc_start: 0.7934 (mmtt) cc_final: 0.7531 (ttmm) REVERT: D 332 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8007 (mt-10) REVERT: D 488 MET cc_start: 0.7798 (mpm) cc_final: 0.7406 (mpp) REVERT: D 661 TYR cc_start: 0.7552 (t80) cc_final: 0.7343 (t80) REVERT: D 671 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7505 (t0) REVERT: D 686 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7454 (pttp) outliers start: 35 outliers final: 8 residues processed: 248 average time/residue: 0.1180 time to fit residues: 48.2594 Evaluate side-chains 196 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 254 TYR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 686 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 26 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 0.0970 chunk 125 optimal weight: 0.0470 chunk 84 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.150229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099911 restraints weight = 33533.376| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.67 r_work: 0.3206 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21000 Z= 0.099 Angle : 0.548 6.885 28288 Z= 0.291 Chirality : 0.036 0.164 3152 Planarity : 0.003 0.043 3468 Dihedral : 16.424 169.380 3168 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.60 % Favored : 93.07 % Rotamer: Outliers : 1.20 % Allowed : 10.70 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.15), residues: 2424 helix: -1.54 (0.12), residues: 1528 sheet: -2.84 (0.52), residues: 88 loop : -2.77 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 226 TYR 0.015 0.001 TYR C 661 PHE 0.024 0.001 PHE B 590 TRP 0.017 0.001 TRP C 493 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (20996) covalent geometry : angle 0.54760 / 0.29 (28280) SS BOND : bond 0.00210 / 0.11 ( 4) SS BOND : angle 0.59093 / 0.39 ( 8) hydrogen bonds : bond 0.03433 / 2.29 ( 761) hydrogen bonds : angle 3.98307 / 2.76 ( 2211) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8626 (tm-30) REVERT: A 161 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7515 (ttmm) REVERT: A 481 TRP cc_start: 0.4967 (m-90) cc_final: 0.4366 (m100) REVERT: A 521 TRP cc_start: 0.7749 (t60) cc_final: 0.7512 (t60) REVERT: A 677 MET cc_start: 0.6727 (mmm) cc_final: 0.5985 (tpt) REVERT: A 686 LYS cc_start: 0.7855 (pttp) cc_final: 0.7556 (ptmm) REVERT: B 141 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8666 (tm-30) REVERT: B 161 LYS cc_start: 0.7978 (mmtt) cc_final: 0.7543 (ttmm) REVERT: B 197 ASN cc_start: 0.8368 (m-40) cc_final: 0.7819 (t0) REVERT: B 481 TRP cc_start: 0.5017 (m-90) cc_final: 0.4334 (m100) REVERT: B 671 ASN cc_start: 0.7874 (OUTLIER) cc_final: 0.7128 (t0) REVERT: B 677 MET cc_start: 0.6645 (mmm) cc_final: 0.6038 (tpt) REVERT: B 686 LYS cc_start: 0.7880 (pttp) cc_final: 0.7580 (ptmm) REVERT: C 161 LYS cc_start: 0.7937 (mmtt) cc_final: 0.7498 (ttmm) REVERT: C 481 TRP cc_start: 0.5015 (m-90) cc_final: 0.4340 (m100) REVERT: C 671 ASN cc_start: 0.7910 (t0) cc_final: 0.7105 (t0) REVERT: D 141 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8637 (tm-30) REVERT: D 161 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7521 (ttmm) REVERT: D 197 ASN cc_start: 0.8381 (m-40) cc_final: 0.7844 (t0) REVERT: D 481 TRP cc_start: 0.4946 (m-90) cc_final: 0.4349 (m100) REVERT: D 671 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7256 (t0) REVERT: D 677 MET cc_start: 0.6738 (mmm) cc_final: 0.5967 (tpt) REVERT: D 686 LYS cc_start: 0.7832 (pttp) cc_final: 0.7543 (ptmm) outliers start: 26 outliers final: 14 residues processed: 235 average time/residue: 0.1205 time to fit residues: 46.4679 Evaluate side-chains 200 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 671 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 71 optimal weight: 3.9990 chunk 165 optimal weight: 30.0000 chunk 150 optimal weight: 0.9980 chunk 192 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 126 optimal weight: 0.0060 chunk 140 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.154542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117625 restraints weight = 32516.589| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.87 r_work: 0.3204 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21000 Z= 0.096 Angle : 0.511 7.893 28288 Z= 0.270 Chirality : 0.036 0.124 3152 Planarity : 0.003 0.041 3468 Dihedral : 15.608 179.349 3168 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.60 % Favored : 93.07 % Rotamer: Outliers : 1.66 % Allowed : 11.25 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.16), residues: 2424 helix: -0.83 (0.13), residues: 1528 sheet: -2.65 (0.54), residues: 88 loop : -2.59 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 226 TYR 0.017 0.001 TYR B 650 PHE 0.014 0.001 PHE B 590 TRP 0.013 0.001 TRP C 493 HIS 0.004 0.001 HIS B 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (20996) covalent geometry : angle 0.51095 / 0.27 (28280) SS BOND : bond 0.00172 / 0.09 ( 4) SS BOND : angle 0.60651 / 0.39 ( 8) hydrogen bonds : bond 0.02871 / 1.91 ( 761) hydrogen bonds : angle 3.70777 / 2.56 ( 2211) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.701 Fit side-chains REVERT: A 141 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8608 (tm-30) REVERT: A 161 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7696 (ttmm) REVERT: A 188 ARG cc_start: 0.8751 (ttm110) cc_final: 0.8444 (ttp-110) REVERT: A 322 ASP cc_start: 0.8783 (t0) cc_final: 0.8217 (m-30) REVERT: A 488 MET cc_start: 0.7367 (mmt) cc_final: 0.7115 (mpp) REVERT: A 652 ILE cc_start: 0.9076 (mt) cc_final: 0.8851 (mm) REVERT: A 677 MET cc_start: 0.6722 (mmm) cc_final: 0.6106 (tpt) REVERT: A 686 LYS cc_start: 0.7909 (pttp) cc_final: 0.7691 (ptmm) REVERT: B 141 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8613 (tm-30) REVERT: B 161 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7736 (ttmm) REVERT: B 188 ARG cc_start: 0.8732 (ttm110) cc_final: 0.8432 (ttp-110) REVERT: B 322 ASP cc_start: 0.8793 (t0) cc_final: 0.8221 (m-30) REVERT: B 488 MET cc_start: 0.7348 (mmt) cc_final: 0.7087 (mpp) REVERT: B 677 MET cc_start: 0.6748 (mmm) cc_final: 0.6201 (tpt) REVERT: B 686 LYS cc_start: 0.7926 (pttp) cc_final: 0.7720 (ptmm) REVERT: C 141 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8632 (tm-30) REVERT: C 161 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7697 (ttmm) REVERT: C 188 ARG cc_start: 0.8769 (ttm110) cc_final: 0.8433 (ttp-110) REVERT: C 488 MET cc_start: 0.7412 (mmt) cc_final: 0.7146 (mpp) REVERT: C 686 LYS cc_start: 0.8154 (ptmm) cc_final: 0.7860 (pttp) REVERT: D 141 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8615 (tm-30) REVERT: D 161 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7734 (ttmm) REVERT: D 188 ARG cc_start: 0.8761 (ttm110) cc_final: 0.8458 (ttp-110) REVERT: D 322 ASP cc_start: 0.8804 (t0) cc_final: 0.8242 (m-30) REVERT: D 488 MET cc_start: 0.7343 (mmt) cc_final: 0.7085 (mpp) REVERT: D 652 ILE cc_start: 0.9086 (mt) cc_final: 0.8857 (mm) REVERT: D 677 MET cc_start: 0.6734 (mmm) cc_final: 0.6068 (tpt) REVERT: D 686 LYS cc_start: 0.7902 (pttp) cc_final: 0.7698 (ptmm) outliers start: 36 outliers final: 17 residues processed: 239 average time/residue: 0.1454 time to fit residues: 54.3806 Evaluate side-chains 208 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 254 TYR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 596 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 136 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 47 optimal weight: 0.0270 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 224 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.155091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.120855 restraints weight = 32774.129| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.87 r_work: 0.3225 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 21000 Z= 0.092 Angle : 0.496 7.392 28288 Z= 0.260 Chirality : 0.036 0.126 3152 Planarity : 0.003 0.039 3468 Dihedral : 14.759 169.040 3168 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.35 % Favored : 93.48 % Rotamer: Outliers : 1.38 % Allowed : 13.28 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.17), residues: 2424 helix: -0.39 (0.14), residues: 1528 sheet: -2.28 (0.59), residues: 84 loop : -2.51 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 226 TYR 0.018 0.001 TYR A 661 PHE 0.016 0.001 PHE C 489 TRP 0.008 0.001 TRP C 493 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.09 (20996) covalent geometry : angle 0.49606 / 0.26 (28280) SS BOND : bond 0.00155 / 0.08 ( 4) SS BOND : angle 0.59068 / 0.38 ( 8) hydrogen bonds : bond 0.02636 / 1.75 ( 761) hydrogen bonds : angle 3.53956 / 2.44 ( 2211) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7808 (ttmm) REVERT: A 652 ILE cc_start: 0.9079 (mt) cc_final: 0.8827 (mm) REVERT: B 141 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8603 (tm-30) REVERT: B 161 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7845 (ttmm) REVERT: B 677 MET cc_start: 0.6727 (mmm) cc_final: 0.5987 (tpt) REVERT: C 161 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7749 (ttmm) REVERT: C 322 ASP cc_start: 0.8548 (t0) cc_final: 0.7985 (m-30) REVERT: C 677 MET cc_start: 0.6603 (mmt) cc_final: 0.6074 (tpt) REVERT: D 161 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7824 (ttmm) REVERT: D 652 ILE cc_start: 0.9105 (mt) cc_final: 0.8858 (mm) outliers start: 30 outliers final: 20 residues processed: 211 average time/residue: 0.1290 time to fit residues: 43.3896 Evaluate side-chains 195 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 596 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 174 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 227 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.150103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.115918 restraints weight = 31996.896| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.65 r_work: 0.3111 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 21000 Z= 0.238 Angle : 0.611 8.513 28288 Z= 0.316 Chirality : 0.041 0.195 3152 Planarity : 0.004 0.052 3468 Dihedral : 14.503 149.115 3168 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.93 % Favored : 92.90 % Rotamer: Outliers : 1.75 % Allowed : 13.33 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.17), residues: 2424 helix: -0.47 (0.13), residues: 1548 sheet: -2.76 (0.55), residues: 88 loop : -2.63 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 226 TYR 0.023 0.002 TYR D 661 PHE 0.025 0.002 PHE B 666 TRP 0.011 0.001 TRP D 521 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 (20996) covalent geometry : angle 0.61131 / 0.32 (28280) SS BOND : bond 0.00087 / 0.04 ( 4) SS BOND : angle 0.63490 / 0.38 ( 8) hydrogen bonds : bond 0.03657 / 2.42 ( 761) hydrogen bonds : angle 3.84609 / 2.64 ( 2211) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.783 Fit side-chains REVERT: A 161 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7993 (ttmm) REVERT: A 197 ASN cc_start: 0.8550 (m-40) cc_final: 0.7922 (t0) REVERT: A 572 MET cc_start: 0.6998 (tpt) cc_final: 0.6178 (tpp) REVERT: A 652 ILE cc_start: 0.9112 (mt) cc_final: 0.8848 (mm) REVERT: B 161 LYS cc_start: 0.8319 (mmtt) cc_final: 0.8024 (ttmm) REVERT: B 572 MET cc_start: 0.6979 (tpt) cc_final: 0.6146 (tpp) REVERT: C 161 LYS cc_start: 0.8258 (mmtt) cc_final: 0.8001 (ttmm) REVERT: C 197 ASN cc_start: 0.8516 (m-40) cc_final: 0.7932 (t0) REVERT: C 572 MET cc_start: 0.6934 (tpt) cc_final: 0.6247 (tpp) REVERT: D 161 LYS cc_start: 0.8327 (mmtt) cc_final: 0.7935 (ttmm) REVERT: D 507 LEU cc_start: 0.7920 (mm) cc_final: 0.7707 (mm) REVERT: D 652 ILE cc_start: 0.9118 (mt) cc_final: 0.8854 (mm) outliers start: 38 outliers final: 24 residues processed: 201 average time/residue: 0.1383 time to fit residues: 45.3965 Evaluate side-chains 193 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 655 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 57 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 198 optimal weight: 0.8980 chunk 125 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 163 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.153663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.117447 restraints weight = 32614.034| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.95 r_work: 0.3183 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21000 Z= 0.090 Angle : 0.492 7.686 28288 Z= 0.261 Chirality : 0.037 0.244 3152 Planarity : 0.003 0.039 3468 Dihedral : 13.775 128.235 3168 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.56 % Favored : 93.28 % Rotamer: Outliers : 1.29 % Allowed : 14.21 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.17), residues: 2424 helix: -0.05 (0.14), residues: 1540 sheet: -2.52 (0.58), residues: 88 loop : -2.55 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 226 TYR 0.022 0.001 TYR C 661 PHE 0.029 0.001 PHE A 666 TRP 0.011 0.001 TRP B 380 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (20996) covalent geometry : angle 0.49172 / 0.26 (28280) SS BOND : bond 0.00076 / 0.04 ( 4) SS BOND : angle 0.62484 / 0.39 ( 8) hydrogen bonds : bond 0.02532 / 1.68 ( 761) hydrogen bonds : angle 3.43451 / 2.38 ( 2211) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.808 Fit side-chains REVERT: A 161 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7864 (ttmm) REVERT: A 197 ASN cc_start: 0.8552 (m-40) cc_final: 0.7955 (t0) REVERT: A 652 ILE cc_start: 0.9036 (mt) cc_final: 0.8761 (mm) REVERT: B 161 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7794 (ttmm) REVERT: B 677 MET cc_start: 0.6606 (mmt) cc_final: 0.5987 (tpt) REVERT: C 161 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7849 (ttmm) REVERT: C 197 ASN cc_start: 0.8528 (m-40) cc_final: 0.8026 (t0) REVERT: D 161 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7894 (ttmm) REVERT: D 507 LEU cc_start: 0.7821 (mm) cc_final: 0.7570 (mm) REVERT: D 652 ILE cc_start: 0.9034 (mt) cc_final: 0.8778 (mm) REVERT: D 677 MET cc_start: 0.6893 (mmm) cc_final: 0.6136 (tpt) outliers start: 28 outliers final: 20 residues processed: 215 average time/residue: 0.1365 time to fit residues: 47.9563 Evaluate side-chains 207 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 655 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 223 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.148759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.108363 restraints weight = 33600.976| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.74 r_work: 0.3148 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21000 Z= 0.154 Angle : 0.547 7.856 28288 Z= 0.284 Chirality : 0.039 0.247 3152 Planarity : 0.003 0.039 3468 Dihedral : 13.605 124.808 3168 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.11 % Favored : 93.73 % Rotamer: Outliers : 1.29 % Allowed : 14.44 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.17), residues: 2424 helix: -0.06 (0.14), residues: 1540 sheet: -2.67 (0.57), residues: 88 loop : -2.52 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 149 TYR 0.017 0.001 TYR C 661 PHE 0.026 0.001 PHE C 449 TRP 0.007 0.001 TRP A 521 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (20996) covalent geometry : angle 0.54649 / 0.28 (28280) SS BOND : bond 0.00102 / 0.05 ( 4) SS BOND : angle 0.60387 / 0.35 ( 8) hydrogen bonds : bond 0.02939 / 1.96 ( 761) hydrogen bonds : angle 3.53245 / 2.43 ( 2211) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.845 Fit side-chains REVERT: A 161 LYS cc_start: 0.8094 (mmtt) cc_final: 0.7839 (ttmm) REVERT: A 197 ASN cc_start: 0.8617 (m-40) cc_final: 0.8114 (t0) REVERT: A 493 TRP cc_start: 0.7110 (OUTLIER) cc_final: 0.6571 (t60) REVERT: A 572 MET cc_start: 0.6737 (tpt) cc_final: 0.6256 (tpp) REVERT: A 652 ILE cc_start: 0.9001 (mt) cc_final: 0.8731 (mm) REVERT: B 161 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7844 (ttmm) REVERT: B 572 MET cc_start: 0.6793 (tpt) cc_final: 0.6399 (tpp) REVERT: C 161 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7790 (ttmm) REVERT: C 197 ASN cc_start: 0.8566 (m-40) cc_final: 0.8125 (t0) REVERT: C 335 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8911 (p) REVERT: C 572 MET cc_start: 0.6759 (tpt) cc_final: 0.6297 (tpp) REVERT: C 677 MET cc_start: 0.6818 (mmt) cc_final: 0.6089 (tpt) REVERT: D 161 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7838 (ttmm) REVERT: D 507 LEU cc_start: 0.7731 (mm) cc_final: 0.7470 (mm) REVERT: D 562 MET cc_start: 0.7693 (mmt) cc_final: 0.7482 (mmp) REVERT: D 572 MET cc_start: 0.6695 (tpt) cc_final: 0.6241 (tpp) REVERT: D 652 ILE cc_start: 0.8947 (mt) cc_final: 0.8653 (mm) REVERT: D 677 MET cc_start: 0.7118 (mmm) cc_final: 0.6267 (tpt) outliers start: 28 outliers final: 20 residues processed: 202 average time/residue: 0.1410 time to fit residues: 46.2079 Evaluate side-chains 201 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 493 TRP Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 655 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 113 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 164 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 GLN D 570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.149056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.108607 restraints weight = 33365.363| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.70 r_work: 0.3160 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21000 Z= 0.144 Angle : 0.538 9.099 28288 Z= 0.280 Chirality : 0.039 0.211 3152 Planarity : 0.003 0.038 3468 Dihedral : 13.311 118.845 3168 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 1.25 % Allowed : 14.39 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.17), residues: 2424 helix: -0.03 (0.14), residues: 1544 sheet: -2.59 (0.56), residues: 88 loop : -2.45 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 226 TYR 0.030 0.002 TYR C 661 PHE 0.026 0.001 PHE C 449 TRP 0.007 0.001 TRP D 481 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (20996) covalent geometry : angle 0.53811 / 0.28 (28280) SS BOND : bond 0.00094 / 0.05 ( 4) SS BOND : angle 0.64292 / 0.38 ( 8) hydrogen bonds : bond 0.02849 / 1.90 ( 761) hydrogen bonds : angle 3.49341 / 2.40 ( 2211) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.779 Fit side-chains REVERT: A 161 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7807 (ttmm) REVERT: A 197 ASN cc_start: 0.8610 (m-40) cc_final: 0.8243 (t0) REVERT: A 335 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8924 (p) REVERT: A 493 TRP cc_start: 0.7130 (OUTLIER) cc_final: 0.6414 (t60) REVERT: A 572 MET cc_start: 0.6646 (tpt) cc_final: 0.6272 (tpp) REVERT: A 652 ILE cc_start: 0.8962 (mt) cc_final: 0.8686 (mm) REVERT: B 161 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7859 (ttmm) REVERT: B 335 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8902 (p) REVERT: B 572 MET cc_start: 0.6661 (tpt) cc_final: 0.6298 (tpp) REVERT: C 161 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7737 (ttmm) REVERT: C 197 ASN cc_start: 0.8576 (m-40) cc_final: 0.8249 (t0) REVERT: C 335 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8938 (p) REVERT: C 572 MET cc_start: 0.6716 (tpt) cc_final: 0.6311 (tpp) REVERT: C 677 MET cc_start: 0.6598 (mmt) cc_final: 0.6049 (tpt) REVERT: D 161 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7842 (ttmm) REVERT: D 335 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8895 (p) REVERT: D 493 TRP cc_start: 0.7190 (OUTLIER) cc_final: 0.6494 (t60) REVERT: D 507 LEU cc_start: 0.7703 (mm) cc_final: 0.7434 (mm) REVERT: D 572 MET cc_start: 0.6583 (tpt) cc_final: 0.6200 (tpp) REVERT: D 652 ILE cc_start: 0.8939 (mt) cc_final: 0.8648 (mm) REVERT: D 677 MET cc_start: 0.7262 (mmm) cc_final: 0.6420 (tpt) outliers start: 27 outliers final: 20 residues processed: 201 average time/residue: 0.1365 time to fit residues: 44.6288 Evaluate side-chains 208 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 493 TRP Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 493 TRP Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 655 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 223 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 158 optimal weight: 7.9990 chunk 3 optimal weight: 0.0170 chunk 93 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN B 570 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.150602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.110038 restraints weight = 33454.820| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.83 r_work: 0.3194 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21000 Z= 0.098 Angle : 0.519 10.574 28288 Z= 0.269 Chirality : 0.037 0.210 3152 Planarity : 0.003 0.038 3468 Dihedral : 13.005 116.037 3168 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.86 % Favored : 93.98 % Rotamer: Outliers : 1.38 % Allowed : 14.16 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.17), residues: 2424 helix: 0.13 (0.14), residues: 1540 sheet: -2.49 (0.58), residues: 88 loop : -2.37 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 226 TYR 0.015 0.001 TYR C 661 PHE 0.034 0.001 PHE B 569 TRP 0.009 0.001 TRP D 380 HIS 0.003 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (20996) covalent geometry : angle 0.51937 / 0.27 (28280) SS BOND : bond 0.00122 / 0.06 ( 4) SS BOND : angle 0.65337 / 0.40 ( 8) hydrogen bonds : bond 0.02484 / 1.66 ( 761) hydrogen bonds : angle 3.37899 / 2.33 ( 2211) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.802 Fit side-chains REVERT: A 161 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7773 (ttmm) REVERT: A 173 MET cc_start: 0.8887 (mtt) cc_final: 0.8613 (mtm) REVERT: A 197 ASN cc_start: 0.8593 (m-40) cc_final: 0.8381 (t0) REVERT: A 335 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8927 (p) REVERT: A 493 TRP cc_start: 0.7015 (OUTLIER) cc_final: 0.6258 (t60) REVERT: A 652 ILE cc_start: 0.8946 (mt) cc_final: 0.8661 (mm) REVERT: B 161 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7843 (ttmm) REVERT: B 173 MET cc_start: 0.8903 (mtt) cc_final: 0.8621 (mtm) REVERT: B 335 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8913 (p) REVERT: C 161 LYS cc_start: 0.8026 (mmtt) cc_final: 0.7690 (ttmm) REVERT: C 335 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8936 (p) REVERT: C 677 MET cc_start: 0.6789 (mmt) cc_final: 0.6106 (tpt) REVERT: D 161 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7817 (ttmm) REVERT: D 173 MET cc_start: 0.8899 (mtt) cc_final: 0.8614 (mtm) REVERT: D 335 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8904 (p) REVERT: D 493 TRP cc_start: 0.7051 (OUTLIER) cc_final: 0.6249 (t60) REVERT: D 507 LEU cc_start: 0.7699 (mm) cc_final: 0.7422 (mm) REVERT: D 572 MET cc_start: 0.6498 (tpt) cc_final: 0.6212 (tpp) REVERT: D 652 ILE cc_start: 0.8923 (mt) cc_final: 0.8629 (mm) REVERT: D 672 MET cc_start: 0.7955 (tmm) cc_final: 0.7528 (tmm) outliers start: 30 outliers final: 21 residues processed: 208 average time/residue: 0.1393 time to fit residues: 47.2091 Evaluate side-chains 215 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 493 TRP Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain D residue 493 TRP Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 655 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 70 optimal weight: 7.9990 chunk 236 optimal weight: 0.0170 chunk 222 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.151324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.110914 restraints weight = 33439.843| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.77 r_work: 0.3194 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21000 Z= 0.110 Angle : 0.527 10.239 28288 Z= 0.271 Chirality : 0.037 0.195 3152 Planarity : 0.003 0.038 3468 Dihedral : 12.856 113.249 3168 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.23 % Favored : 93.61 % Rotamer: Outliers : 1.29 % Allowed : 14.35 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.17), residues: 2424 helix: 0.19 (0.14), residues: 1544 sheet: -2.47 (0.57), residues: 88 loop : -2.33 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 226 TYR 0.031 0.001 TYR C 661 PHE 0.030 0.001 PHE B 569 TRP 0.006 0.001 TRP B 493 HIS 0.003 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (20996) covalent geometry : angle 0.52663 / 0.27 (28280) SS BOND : bond 0.00116 / 0.06 ( 4) SS BOND : angle 0.65785 / 0.40 ( 8) hydrogen bonds : bond 0.02569 / 1.71 ( 761) hydrogen bonds : angle 3.38801 / 2.34 ( 2211) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4888.48 seconds wall clock time: 84 minutes 28.40 seconds (5068.40 seconds total)