Starting phenix.real_space_refine on Sat Jan 18 08:24:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l3h_0822/01_2025/6l3h_0822.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l3h_0822/01_2025/6l3h_0822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6l3h_0822/01_2025/6l3h_0822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l3h_0822/01_2025/6l3h_0822.map" model { file = "/net/cci-nas-00/data/ceres_data/6l3h_0822/01_2025/6l3h_0822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l3h_0822/01_2025/6l3h_0822.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 Ca 2 9.91 5 Fe 6 7.16 5 S 50 5.16 5 C 7950 2.51 5 N 1902 2.21 5 O 2056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11966 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5895 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 711} Chain breaks: 1 Chain: "B" Number of atoms: 5895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5895 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 711} Chain breaks: 1 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.26, per 1000 atoms: 0.61 Number of scatterers: 11966 At special positions: 0 Unit cell: (75.97, 114.49, 107, 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) Fe 6 26.01 Ca 2 19.99 S 50 16.00 O 2056 8.00 N 1902 7.00 C 7950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.6 seconds 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 4 sheets defined 71.0% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 4 through 25 removed outlier: 3.582A pdb=" N VAL A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 33 removed outlier: 3.540A pdb=" N ALA A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.532A pdb=" N GLN A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 removed outlier: 7.121A pdb=" N MET A 67 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 69 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 removed outlier: 3.552A pdb=" N HIS A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 127 removed outlier: 4.313A pdb=" N ASP A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 161 removed outlier: 3.511A pdb=" N LYS A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.600A pdb=" N GLU A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 removed outlier: 3.527A pdb=" N PHE A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.614A pdb=" N ASN A 222 " --> pdb=" O PRO A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 254 removed outlier: 3.677A pdb=" N TYR A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 236 " --> pdb=" O TRP A 232 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 279 Processing helix chain 'A' and resid 280 through 288 removed outlier: 3.566A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 302 removed outlier: 3.708A pdb=" N VAL A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.982A pdb=" N TRP A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 359 removed outlier: 4.097A pdb=" N ALA A 339 " --> pdb=" O HIS A 335 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 366 through 394 removed outlier: 3.538A pdb=" N LEU A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 416 through 437 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.719A pdb=" N PHE A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 463 " --> pdb=" O MET A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 477 through 485 removed outlier: 3.709A pdb=" N TYR A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.548A pdb=" N PHE A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR A 502 " --> pdb=" O GLU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 534 removed outlier: 3.525A pdb=" N THR A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 525 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N MET A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 543 Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.930A pdb=" N ALA A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 569 removed outlier: 4.265A pdb=" N LEU A 569 " --> pdb=" O VAL A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 580 removed outlier: 3.695A pdb=" N TYR A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A 576 " --> pdb=" O ARG A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 584 removed outlier: 4.346A pdb=" N SER A 584 " --> pdb=" O GLN A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 591 through 607 removed outlier: 3.508A pdb=" N ALA A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 removed outlier: 4.190A pdb=" N TYR A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 655 removed outlier: 4.516A pdb=" N PHE A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 685 removed outlier: 3.805A pdb=" N TRP A 670 " --> pdb=" O LYS A 666 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP A 673 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 701 removed outlier: 3.618A pdb=" N ALA A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'A' and resid 723 through 746 removed outlier: 3.954A pdb=" N ALA A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.583A pdb=" N VAL B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 33 removed outlier: 3.540A pdb=" N ALA B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 removed outlier: 3.533A pdb=" N GLN B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 69 removed outlier: 7.120A pdb=" N MET B 67 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 69 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 100 removed outlier: 3.552A pdb=" N HIS B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 127 removed outlier: 4.314A pdb=" N ASP B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 161 removed outlier: 3.509A pdb=" N LYS B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 153 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Proline residue: B 154 - end of helix Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.600A pdb=" N GLU B 187 " --> pdb=" O GLN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 200 removed outlier: 3.525A pdb=" N PHE B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.614A pdb=" N ASN B 222 " --> pdb=" O PRO B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 254 removed outlier: 3.678A pdb=" N TYR B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 279 Processing helix chain 'B' and resid 280 through 288 removed outlier: 3.566A pdb=" N VAL B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 302 removed outlier: 3.708A pdb=" N VAL B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.982A pdb=" N TRP B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 359 removed outlier: 4.098A pdb=" N ALA B 339 " --> pdb=" O HIS B 335 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 366 through 394 removed outlier: 3.567A pdb=" N GLY B 370 " --> pdb=" O PHE B 366 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B 394 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 401 through 406 Processing helix chain 'B' and resid 416 through 437 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 449 through 465 removed outlier: 3.720A pdb=" N PHE B 455 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 463 " --> pdb=" O MET B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 477 through 485 removed outlier: 3.709A pdb=" N TYR B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 488 No H-bonds generated for 'chain 'B' and resid 486 through 488' Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.549A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR B 502 " --> pdb=" O GLU B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 534 removed outlier: 3.525A pdb=" N THR B 521 " --> pdb=" O ARG B 517 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 525 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 534 " --> pdb=" O ILE B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 551 through 560 removed outlier: 3.930A pdb=" N ALA B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 569 removed outlier: 4.266A pdb=" N LEU B 569 " --> pdb=" O VAL B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 580 removed outlier: 3.694A pdb=" N TYR B 575 " --> pdb=" O GLY B 571 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 removed outlier: 4.347A pdb=" N SER B 584 " --> pdb=" O GLN B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 584' Processing helix chain 'B' and resid 591 through 607 removed outlier: 3.507A pdb=" N ALA B 601 " --> pdb=" O PHE B 597 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 removed outlier: 4.189A pdb=" N TYR B 623 " --> pdb=" O ILE B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 655 removed outlier: 4.516A pdb=" N PHE B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 685 removed outlier: 3.805A pdb=" N TRP B 670 " --> pdb=" O LYS B 666 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP B 673 " --> pdb=" O THR B 669 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 680 " --> pdb=" O ASN B 676 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 701 removed outlier: 3.618A pdb=" N ALA B 697 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 698 " --> pdb=" O GLN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 707 Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'B' and resid 723 through 746 removed outlier: 3.955A pdb=" N ALA B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE B 730 " --> pdb=" O ALA B 726 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 746 " --> pdb=" O ALA B 742 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 removed outlier: 6.661A pdb=" N GLN A 39 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE A 141 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 41 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.664A pdb=" N HIS A 75 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 48 removed outlier: 6.661A pdb=" N GLN B 39 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE B 141 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 41 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.664A pdb=" N HIS B 75 " --> pdb=" O VAL B 72 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1779 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: 3.82 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 4553 1.37 - 1.54: 7683 1.54 - 1.71: 26 1.71 - 1.88: 90 1.88 - 2.05: 16 Bond restraints: 12368 Sorted by residual: bond pdb=" C ARG A 368 " pdb=" O ARG A 368 " ideal model delta sigma weight residual 1.236 1.204 0.032 1.25e-02 6.40e+03 6.68e+00 bond pdb=" N LYS A 365 " pdb=" CA LYS A 365 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.24e+00 bond pdb=" N SER B 44 " pdb=" CA SER B 44 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.75e+00 bond pdb=" N TRP A 722 " pdb=" CA TRP A 722 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.27e-02 6.20e+03 5.69e+00 bond pdb=" N LYS B 365 " pdb=" CA LYS B 365 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.66e+00 ... (remaining 12363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 16708 2.81 - 5.63: 192 5.63 - 8.44: 10 8.44 - 11.26: 2 11.26 - 14.07: 4 Bond angle restraints: 16916 Sorted by residual: angle pdb=" N TRP A 722 " pdb=" CA TRP A 722 " pdb=" C TRP A 722 " ideal model delta sigma weight residual 113.41 107.56 5.85 1.22e+00 6.72e-01 2.30e+01 angle pdb=" N TRP B 722 " pdb=" CA TRP B 722 " pdb=" C TRP B 722 " ideal model delta sigma weight residual 113.41 107.58 5.83 1.22e+00 6.72e-01 2.28e+01 angle pdb=" N ILE B 606 " pdb=" CA ILE B 606 " pdb=" C ILE B 606 " ideal model delta sigma weight residual 112.96 108.23 4.73 1.00e+00 1.00e+00 2.24e+01 angle pdb=" N ILE A 606 " pdb=" CA ILE A 606 " pdb=" C ILE A 606 " ideal model delta sigma weight residual 112.96 108.24 4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" N VAL A 723 " pdb=" CA VAL A 723 " pdb=" C VAL A 723 " ideal model delta sigma weight residual 113.07 107.75 5.32 1.36e+00 5.41e-01 1.53e+01 ... (remaining 16911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 6199 17.26 - 34.52: 558 34.52 - 51.79: 87 51.79 - 69.05: 24 69.05 - 86.31: 10 Dihedral angle restraints: 6878 sinusoidal: 2622 harmonic: 4256 Sorted by residual: dihedral pdb=" CA PHE B 471 " pdb=" C PHE B 471 " pdb=" N TYR B 472 " pdb=" CA TYR B 472 " ideal model delta harmonic sigma weight residual 180.00 147.83 32.17 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA PHE A 471 " pdb=" C PHE A 471 " pdb=" N TYR A 472 " pdb=" CA TYR A 472 " ideal model delta harmonic sigma weight residual 180.00 147.86 32.14 0 5.00e+00 4.00e-02 4.13e+01 dihedral pdb=" CA GLU B 265 " pdb=" C GLU B 265 " pdb=" N ASP B 266 " pdb=" CA ASP B 266 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 6875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1071 0.038 - 0.077: 575 0.077 - 0.115: 142 0.115 - 0.154: 16 0.154 - 0.192: 4 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CA TRP B 722 " pdb=" N TRP B 722 " pdb=" C TRP B 722 " pdb=" CB TRP B 722 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA TRP A 722 " pdb=" N TRP A 722 " pdb=" C TRP A 722 " pdb=" CB TRP A 722 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CA PHE A 471 " pdb=" N PHE A 471 " pdb=" C PHE A 471 " pdb=" CB PHE A 471 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 1805 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 471 " -0.023 2.00e-02 2.50e+03 1.71e-02 5.11e+00 pdb=" CG PHE A 471 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 471 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 471 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 471 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 471 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 471 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 471 " 0.023 2.00e-02 2.50e+03 1.70e-02 5.06e+00 pdb=" CG PHE B 471 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE B 471 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 471 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 471 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 471 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 471 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 153 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.53e+00 pdb=" N PRO B 154 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " -0.026 5.00e-02 4.00e+02 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 80 2.61 - 3.18: 10446 3.18 - 3.75: 17570 3.75 - 4.33: 27358 4.33 - 4.90: 44298 Nonbonded interactions: 99752 Sorted by model distance: nonbonded pdb=" ND1 HIS B 490 " pdb="FE FE B 803 " model vdw 2.036 2.340 nonbonded pdb=" ND1 HIS A 490 " pdb="FE FE A 803 " model vdw 2.036 2.340 nonbonded pdb=" OG SER A 338 " pdb=" OH TYR A 386 " model vdw 2.094 3.040 nonbonded pdb=" OG SER B 338 " pdb=" OH TYR B 386 " model vdw 2.096 3.040 nonbonded pdb=" OE1 GLU B 494 " pdb="FE FE B 803 " model vdw 2.157 2.260 ... (remaining 99747 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.180 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 : 0.007 0.070 12368 Z= 0.464 Angle : 0.767 14.073 16916 Z= 0.412 Chirality : 0.047 0.192 1808 Planarity : 0.004 0.047 2080 Dihedral : 13.750 86.311 4166 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.16 % Allowed : 3.13 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.18), residues: 1474 helix: -2.86 (0.13), residues: 978 sheet: None (None), residues: 0 loop : -3.08 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 342 HIS 0.008 0.001 HIS B 157 PHE 0.038 0.002 PHE A 471 TYR 0.015 0.002 TYR A 328 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 1.336 Fit side-chains REVERT: A 365 LYS cc_start: 0.5545 (mttt) cc_final: 0.5007 (mptt) REVERT: A 682 MET cc_start: 0.8798 (ptt) cc_final: 0.8446 (ptt) REVERT: B 365 LYS cc_start: 0.5827 (mttt) cc_final: 0.5487 (mtpt) REVERT: B 682 MET cc_start: 0.8774 (ptt) cc_final: 0.8402 (ptt) REVERT: B 728 ASP cc_start: 0.7381 (m-30) cc_final: 0.7131 (m-30) outliers start: 2 outliers final: 2 residues processed: 119 average time/residue: 0.2820 time to fit residues: 46.8379 Evaluate side-chains 90 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 722 TRP Chi-restraints excluded: chain B residue 722 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 GLN B 741 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.083191 restraints weight = 16032.547| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 1.60 r_work: 0.2699 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12368 Z= 0.191 Angle : 0.596 7.270 16916 Z= 0.310 Chirality : 0.040 0.151 1808 Planarity : 0.005 0.050 2080 Dihedral : 7.439 74.167 1624 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.07 % Allowed : 7.66 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.20), residues: 1474 helix: -1.41 (0.15), residues: 1014 sheet: None (None), residues: 0 loop : -2.74 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 342 HIS 0.005 0.001 HIS B 541 PHE 0.021 0.001 PHE B 471 TYR 0.014 0.001 TYR B 510 ARG 0.003 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.320 Fit side-chains REVERT: A 365 LYS cc_start: 0.5141 (mttt) cc_final: 0.4436 (mmmt) REVERT: A 563 GLU cc_start: 0.8743 (tt0) cc_final: 0.8506 (tt0) REVERT: B 322 MET cc_start: 0.8094 (tpt) cc_final: 0.7863 (tpt) outliers start: 13 outliers final: 6 residues processed: 118 average time/residue: 0.2333 time to fit residues: 42.2026 Evaluate side-chains 101 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 722 TRP Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 722 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 0.0270 chunk 35 optimal weight: 0.8980 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.104173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.082625 restraints weight = 16160.553| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.63 r_work: 0.2695 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12368 Z= 0.210 Angle : 0.590 11.662 16916 Z= 0.291 Chirality : 0.041 0.152 1808 Planarity : 0.004 0.043 2080 Dihedral : 7.244 74.403 1624 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.74 % Allowed : 10.13 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.21), residues: 1474 helix: -0.54 (0.16), residues: 1012 sheet: None (None), residues: 0 loop : -2.48 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 342 HIS 0.007 0.001 HIS A 541 PHE 0.024 0.001 PHE A 471 TYR 0.012 0.001 TYR B 328 ARG 0.003 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.314 Fit side-chains REVERT: A 365 LYS cc_start: 0.5289 (mttt) cc_final: 0.4467 (mmmt) REVERT: A 715 GLU cc_start: 0.8434 (tp30) cc_final: 0.8174 (tp30) REVERT: A 728 ASP cc_start: 0.7471 (m-30) cc_final: 0.7254 (m-30) REVERT: B 322 MET cc_start: 0.8089 (tpt) cc_final: 0.7823 (tpt) REVERT: B 715 GLU cc_start: 0.8434 (tp30) cc_final: 0.8174 (tp30) REVERT: B 728 ASP cc_start: 0.7405 (m-30) cc_final: 0.7168 (m-30) outliers start: 9 outliers final: 5 residues processed: 108 average time/residue: 0.2243 time to fit residues: 37.4024 Evaluate side-chains 101 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 142 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.088870 restraints weight = 15549.859| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.59 r_work: 0.2736 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12368 Z= 0.157 Angle : 0.533 9.588 16916 Z= 0.267 Chirality : 0.039 0.141 1808 Planarity : 0.004 0.041 2080 Dihedral : 6.720 74.150 1620 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.74 % Allowed : 10.46 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1474 helix: 0.06 (0.17), residues: 1006 sheet: None (None), residues: 0 loop : -2.14 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 342 HIS 0.007 0.001 HIS B 541 PHE 0.017 0.001 PHE B 471 TYR 0.011 0.001 TYR B 472 ARG 0.002 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.265 Fit side-chains REVERT: A 471 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7655 (p90) REVERT: A 715 GLU cc_start: 0.8407 (tp30) cc_final: 0.8130 (tp30) REVERT: B 322 MET cc_start: 0.8000 (tpt) cc_final: 0.7675 (tpt) REVERT: B 471 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7634 (p90) REVERT: B 715 GLU cc_start: 0.8408 (tp30) cc_final: 0.8133 (tp30) REVERT: B 728 ASP cc_start: 0.7425 (m-30) cc_final: 0.7183 (m-30) outliers start: 9 outliers final: 3 residues processed: 120 average time/residue: 0.2061 time to fit residues: 38.3774 Evaluate side-chains 111 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 471 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 23 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.105935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.084260 restraints weight = 15912.872| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.61 r_work: 0.2740 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12368 Z= 0.177 Angle : 0.556 12.047 16916 Z= 0.270 Chirality : 0.040 0.146 1808 Planarity : 0.004 0.042 2080 Dihedral : 6.653 73.781 1620 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.07 % Allowed : 11.29 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1474 helix: 0.29 (0.17), residues: 1018 sheet: None (None), residues: 0 loop : -2.12 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 342 HIS 0.007 0.001 HIS A 541 PHE 0.021 0.001 PHE B 471 TYR 0.011 0.001 TYR A 472 ARG 0.002 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 1.257 Fit side-chains REVERT: A 265 GLU cc_start: 0.8241 (pt0) cc_final: 0.7384 (tp30) REVERT: A 471 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7771 (p90) REVERT: A 715 GLU cc_start: 0.8395 (tp30) cc_final: 0.8120 (tp30) REVERT: B 322 MET cc_start: 0.7996 (tpt) cc_final: 0.7697 (tpt) REVERT: B 471 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7750 (p90) REVERT: B 715 GLU cc_start: 0.8439 (tp30) cc_final: 0.8139 (tp30) REVERT: B 728 ASP cc_start: 0.7470 (m-30) cc_final: 0.7244 (m-30) outliers start: 13 outliers final: 7 residues processed: 116 average time/residue: 0.2171 time to fit residues: 38.7717 Evaluate side-chains 113 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 553 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8888 > 50: distance: 57 - 61: 29.633 distance: 61 - 62: 25.435 distance: 62 - 63: 16.135 distance: 62 - 65: 19.976 distance: 63 - 64: 37.892 distance: 63 - 70: 26.695 distance: 65 - 66: 20.487 distance: 66 - 67: 16.262 distance: 67 - 69: 39.821 distance: 70 - 71: 37.740 distance: 71 - 72: 9.381 distance: 71 - 74: 30.290 distance: 72 - 84: 50.476 distance: 74 - 75: 28.763 distance: 75 - 76: 31.232 distance: 75 - 77: 10.085 distance: 76 - 78: 12.711 distance: 77 - 79: 10.303 distance: 77 - 80: 18.323 distance: 78 - 79: 19.805 distance: 79 - 81: 10.212 distance: 80 - 82: 15.832 distance: 81 - 83: 16.847 distance: 82 - 83: 15.395 distance: 84 - 85: 30.021 distance: 85 - 86: 59.449 distance: 85 - 88: 39.820 distance: 86 - 87: 21.768 distance: 86 - 89: 22.607 distance: 89 - 90: 35.064 distance: 90 - 93: 7.829 distance: 91 - 92: 41.227 distance: 93 - 94: 65.848 distance: 94 - 95: 35.875 distance: 95 - 96: 3.311 distance: 96 - 97: 57.244 distance: 98 - 99: 9.196 distance: 99 - 100: 11.706 distance: 99 - 102: 30.333 distance: 100 - 101: 18.514 distance: 100 - 109: 4.086 distance: 102 - 103: 16.760 distance: 103 - 104: 23.024 distance: 104 - 105: 12.317 distance: 105 - 106: 10.375 distance: 106 - 107: 12.057 distance: 106 - 108: 15.599 distance: 109 - 110: 7.064 distance: 110 - 111: 6.667 distance: 110 - 113: 20.023 distance: 111 - 112: 42.513 distance: 111 - 117: 25.057 distance: 113 - 114: 51.489 distance: 114 - 115: 41.047 distance: 117 - 118: 35.907 distance: 118 - 119: 35.700 distance: 118 - 121: 43.325 distance: 119 - 128: 40.381 distance: 120 - 157: 32.303 distance: 121 - 122: 11.289 distance: 122 - 123: 18.742 distance: 123 - 124: 42.813 distance: 124 - 125: 39.473 distance: 125 - 126: 61.359 distance: 128 - 129: 4.120 distance: 129 - 130: 17.339 distance: 129 - 132: 25.728 distance: 130 - 131: 22.273 distance: 130 - 142: 40.727 distance: 131 - 165: 34.879 distance: 132 - 133: 32.588 distance: 133 - 134: 14.072 distance: 133 - 135: 15.951 distance: 134 - 136: 21.160 distance: 135 - 137: 21.168 distance: 135 - 138: 30.859 distance: 136 - 137: 25.264 distance: 137 - 139: 22.748 distance: 138 - 140: 8.075 distance: 139 - 141: 53.127 distance: 140 - 141: 15.305 distance: 142 - 148: 41.292 distance: 143 - 144: 21.356 distance: 143 - 146: 3.634 distance: 144 - 145: 20.089 distance: 144 - 149: 12.946 distance: 145 - 171: 34.654 distance: 147 - 148: 45.281 distance: 149 - 150: 24.203 distance: 150 - 151: 33.824 distance: 150 - 153: 28.957 distance: 151 - 152: 8.799 distance: 151 - 157: 27.888 distance: 152 - 182: 32.749 distance: 153 - 154: 6.596 distance: 154 - 155: 35.493 distance: 154 - 156: 32.949