Starting phenix.real_space_refine on Wed Jul 30 04:30:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l3h_0822/07_2025/6l3h_0822.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l3h_0822/07_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_0822/07_2025/6l3h_0822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l3h_0822/07_2025/6l3h_0822.map" model { file = "/net/cci-nas-00/data/ceres_data/6l3h_0822/07_2025/6l3h_0822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l3h_0822/07_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.07, per 1000 atoms: 0.67 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: 5.06 Conformation dependent library (CDL) restraints added in 2.9 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: 1.15 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: 3.33 Time building geometry restraints manager: 5.79 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: 0.06 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: 0.590 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.820 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.110 ------------------------------------------------------------------------------- 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 : 0.009 0.346 12372 Z= 0.309 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 Details of bonding type rmsd hydrogen bonds : bond 0.25183 ( 613) hydrogen bonds : angle 8.24167 ( 1779) covalent geometry : bond 0.00725 (12368) covalent geometry : angle 0.76745 (16916) Misc. bond : bond 0.33162 ( 4) *********************** 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 : 1.373 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: 0.2987 time to fit residues: 50.0408 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 : 1.283 ------------------------------------------------------------------------------- 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: 0.0870 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: 3.9990 chunk 86 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- 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 = 0.3123 r_free = 0.3123 target = 0.104722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.083412 restraints weight = 16002.762| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.59 r_work: 0.2706 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12372 Z= 0.131 Angle : 0.594 7.435 16916 Z= 0.311 Chirality : 0.040 0.148 1808 Planarity : 0.005 0.051 2080 Dihedral : 7.437 73.597 1624 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % 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: -2.83 (0.20), residues: 1474 helix: -1.38 (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 0.006 0.001 HIS B 541 PHE 0.020 0.001 PHE A 471 TYR 0.013 0.001 TYR B 510 ARG 0.004 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.05473 ( 613) hydrogen bonds : angle 4.93729 ( 1779) covalent geometry : bond 0.00277 (12368) covalent geometry : angle 0.59439 (16916) Misc. bond : bond 0.03292 ( 4) *********************** 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 123 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.370 Fit side-chains REVERT: A 365 LYS cc_start: 0.5154 (mttt) cc_final: 0.4444 (mmmt) REVERT: A 563 GLU cc_start: 0.8742 (tt0) cc_final: 0.8512 (tt0) outliers start: 13 outliers final: 5 residues processed: 116 average time/residue: 0.2394 time to fit residues: 42.5775 Evaluate side-chains 102 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 48 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.103346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.081795 restraints weight = 16185.225| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.61 r_work: 0.2687 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12372 Z= 0.144 Angle : 0.606 12.500 16916 Z= 0.297 Chirality : 0.041 0.156 1808 Planarity : 0.004 0.043 2080 Dihedral : 7.268 74.784 1624 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.66 % Allowed : 9.88 % Favored : 89.46 % 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: -1.76 (0.21), residues: 1474 helix: -0.51 (0.17), residues: 1012 sheet: None (None), residues: 0 loop : -2.49 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 342 HIS 0.006 0.001 HIS A 541 PHE 0.026 0.001 PHE A 471 TYR 0.013 0.001 TYR B 328 ARG 0.003 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 613) hydrogen bonds : angle 4.57149 ( 1779) covalent geometry : bond 0.00351 (12368) covalent geometry : angle 0.60589 (16916) Misc. bond : bond 0.02815 ( 4) *********************** 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: 8 poor density : 104 time to evaluate : 1.332 Fit side-chains REVERT: A 365 LYS cc_start: 0.5302 (mttt) cc_final: 0.4466 (mmmt) REVERT: A 715 GLU cc_start: 0.8428 (tp30) cc_final: 0.8155 (tp30) REVERT: A 728 ASP cc_start: 0.7424 (m-30) cc_final: 0.7212 (m-30) REVERT: B 715 GLU cc_start: 0.8453 (tp30) cc_final: 0.8180 (tp30) REVERT: B 728 ASP cc_start: 0.7405 (m-30) cc_final: 0.7169 (m-30) outliers start: 8 outliers final: 4 residues processed: 108 average time/residue: 0.2081 time to fit residues: 34.5848 Evaluate side-chains 100 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 GLU 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: 0.9980 chunk 102 optimal weight: 5.9990 chunk 18 optimal weight: 0.0970 chunk 29 optimal weight: 0.0980 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 178 ASN B 741 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.110824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.089453 restraints weight = 15465.493| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.59 r_work: 0.2777 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 12372 Z= 0.103 Angle : 0.525 8.990 16916 Z= 0.265 Chirality : 0.039 0.140 1808 Planarity : 0.004 0.041 2080 Dihedral : 6.699 74.227 1620 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.91 % Allowed : 10.46 % Favored : 88.63 % 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: -0.92 (0.22), residues: 1474 helix: 0.09 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -2.07 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 342 HIS 0.008 0.001 HIS B 541 PHE 0.016 0.001 PHE B 471 TYR 0.011 0.001 TYR B 472 ARG 0.002 0.000 ARG A 436 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 613) hydrogen bonds : angle 4.19016 ( 1779) covalent geometry : bond 0.00233 (12368) covalent geometry : angle 0.52519 (16916) Misc. bond : bond 0.03298 ( 4) *********************** 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 126 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 1.323 Fit side-chains REVERT: A 265 GLU cc_start: 0.8146 (pt0) cc_final: 0.7531 (tp30) REVERT: A 471 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7666 (p90) REVERT: A 715 GLU cc_start: 0.8354 (tp30) cc_final: 0.8073 (tp30) REVERT: B 265 GLU cc_start: 0.8108 (pt0) cc_final: 0.7490 (tp30) REVERT: B 471 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7646 (p90) REVERT: B 715 GLU cc_start: 0.8358 (tp30) cc_final: 0.8078 (tp30) REVERT: B 728 ASP cc_start: 0.7432 (m-30) cc_final: 0.7204 (m-30) outliers start: 11 outliers final: 4 residues processed: 123 average time/residue: 0.2054 time to fit residues: 39.1887 Evaluate side-chains 113 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 665 ASP 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: 0.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.087851 restraints weight = 15625.789| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.60 r_work: 0.2774 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12372 Z= 0.107 Angle : 0.548 11.724 16916 Z= 0.266 Chirality : 0.039 0.144 1808 Planarity : 0.004 0.042 2080 Dihedral : 6.611 73.822 1620 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.40 % Allowed : 11.29 % Favored : 87.31 % 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: -0.63 (0.23), residues: 1474 helix: 0.34 (0.17), residues: 1018 sheet: None (None), residues: 0 loop : -2.06 (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 0.020 0.001 PHE A 471 TYR 0.010 0.001 TYR A 472 ARG 0.002 0.000 ARG B 591 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 613) hydrogen bonds : angle 4.10810 ( 1779) covalent geometry : bond 0.00254 (12368) covalent geometry : angle 0.54812 (16916) Misc. bond : bond 0.02562 ( 4) *********************** 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 130 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.400 Fit side-chains REVERT: A 265 GLU cc_start: 0.8068 (pt0) cc_final: 0.7533 (tp30) REVERT: A 471 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7697 (p90) REVERT: A 715 GLU cc_start: 0.8367 (tp30) cc_final: 0.8097 (tp30) REVERT: B 265 GLU cc_start: 0.8064 (pt0) cc_final: 0.7524 (tp30) REVERT: B 471 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7668 (p90) REVERT: B 496 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.7476 (t80) REVERT: B 715 GLU cc_start: 0.8364 (tp30) cc_final: 0.8095 (tp30) REVERT: B 728 ASP cc_start: 0.7464 (m-30) cc_final: 0.7248 (m-30) outliers start: 17 outliers final: 10 residues processed: 123 average time/residue: 0.2142 time to fit residues: 40.7451 Evaluate side-chains 123 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 318 LEU 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 262 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 605 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 55 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.111421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.089629 restraints weight = 15691.345| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.64 r_work: 0.2780 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12372 Z= 0.102 Angle : 0.531 10.739 16916 Z= 0.261 Chirality : 0.039 0.142 1808 Planarity : 0.004 0.042 2080 Dihedral : 6.546 73.638 1620 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.48 % Allowed : 11.78 % Favored : 86.74 % 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: -0.31 (0.23), residues: 1474 helix: 0.57 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -1.95 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 342 HIS 0.007 0.001 HIS A 541 PHE 0.018 0.001 PHE B 471 TYR 0.010 0.001 TYR A 472 ARG 0.002 0.000 ARG B 436 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 613) hydrogen bonds : angle 4.02242 ( 1779) covalent geometry : bond 0.00240 (12368) covalent geometry : angle 0.53123 (16916) Misc. bond : bond 0.02336 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 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 137 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.269 Fit side-chains REVERT: A 265 GLU cc_start: 0.8134 (pt0) cc_final: 0.7568 (tp30) REVERT: A 471 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7624 (p90) REVERT: A 496 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7360 (t80) REVERT: A 563 GLU cc_start: 0.8237 (tt0) cc_final: 0.7975 (tt0) REVERT: A 715 GLU cc_start: 0.8388 (tp30) cc_final: 0.8142 (tp30) REVERT: B 265 GLU cc_start: 0.8129 (pt0) cc_final: 0.7571 (tp30) REVERT: B 471 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7616 (p90) REVERT: B 496 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7501 (t80) REVERT: B 715 GLU cc_start: 0.8384 (tp30) cc_final: 0.8143 (tp30) REVERT: B 728 ASP cc_start: 0.7460 (m-30) cc_final: 0.7254 (m-30) outliers start: 18 outliers final: 10 residues processed: 130 average time/residue: 0.2224 time to fit residues: 43.5922 Evaluate side-chains 129 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 318 LEU Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 665 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 32 optimal weight: 0.7980 chunk 120 optimal weight: 0.2980 chunk 134 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 40 optimal weight: 0.0870 chunk 56 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.109938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.088151 restraints weight = 15774.408| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.63 r_work: 0.2809 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12372 Z= 0.096 Angle : 0.520 10.208 16916 Z= 0.256 Chirality : 0.039 0.137 1808 Planarity : 0.004 0.041 2080 Dihedral : 6.465 73.858 1620 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.07 % Allowed : 12.52 % Favored : 86.41 % 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: -0.01 (0.23), residues: 1474 helix: 0.80 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -1.84 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 342 HIS 0.007 0.001 HIS A 541 PHE 0.017 0.001 PHE A 471 TYR 0.009 0.001 TYR B 472 ARG 0.002 0.000 ARG B 436 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 613) hydrogen bonds : angle 3.94800 ( 1779) covalent geometry : bond 0.00220 (12368) covalent geometry : angle 0.52026 (16916) Misc. bond : bond 0.01999 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 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 137 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 1.318 Fit side-chains REVERT: A 265 GLU cc_start: 0.8116 (pt0) cc_final: 0.7491 (tp30) REVERT: A 471 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7561 (p90) REVERT: A 496 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7352 (t80) REVERT: A 715 GLU cc_start: 0.8374 (tp30) cc_final: 0.8139 (tp30) REVERT: B 265 GLU cc_start: 0.8091 (pt0) cc_final: 0.7462 (tp30) REVERT: B 471 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7508 (p90) REVERT: B 496 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7338 (t80) REVERT: B 715 GLU cc_start: 0.8383 (tp30) cc_final: 0.8168 (tp30) outliers start: 13 outliers final: 8 residues processed: 131 average time/residue: 0.2276 time to fit residues: 45.4382 Evaluate side-chains 133 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 A residue 496 PHE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 605 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 33 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.109813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.088005 restraints weight = 15882.174| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.63 r_work: 0.2813 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12372 Z= 0.099 Angle : 0.528 11.081 16916 Z= 0.257 Chirality : 0.039 0.139 1808 Planarity : 0.004 0.041 2080 Dihedral : 6.448 73.464 1620 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.73 % Allowed : 12.44 % Favored : 85.83 % 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: 0.15 (0.23), residues: 1474 helix: 0.93 (0.17), residues: 1022 sheet: None (None), residues: 0 loop : -1.79 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 342 HIS 0.007 0.001 HIS A 541 PHE 0.018 0.001 PHE B 471 TYR 0.009 0.001 TYR A 472 ARG 0.002 0.000 ARG B 436 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 613) hydrogen bonds : angle 3.93754 ( 1779) covalent geometry : bond 0.00234 (12368) covalent geometry : angle 0.52833 (16916) Misc. bond : bond 0.02289 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 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 146 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.422 Fit side-chains REVERT: A 130 GLN cc_start: 0.5365 (mm-40) cc_final: 0.4871 (pp30) REVERT: A 265 GLU cc_start: 0.8133 (pt0) cc_final: 0.7532 (tp30) REVERT: A 379 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7104 (m-80) REVERT: A 471 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7519 (p90) REVERT: B 130 GLN cc_start: 0.5390 (mm-40) cc_final: 0.4876 (pp30) REVERT: B 265 GLU cc_start: 0.8072 (pt0) cc_final: 0.7544 (tp30) REVERT: B 318 LEU cc_start: 0.5088 (OUTLIER) cc_final: 0.4462 (mp) REVERT: B 471 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7519 (p90) outliers start: 21 outliers final: 12 residues processed: 136 average time/residue: 0.2270 time to fit residues: 46.4150 Evaluate side-chains 140 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 318 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 435 LEU 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 262 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 605 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 14 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 92 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 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 581 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.109632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.087780 restraints weight = 15811.227| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.64 r_work: 0.2809 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12372 Z= 0.097 Angle : 0.528 10.687 16916 Z= 0.257 Chirality : 0.039 0.137 1808 Planarity : 0.004 0.041 2080 Dihedral : 6.408 73.496 1620 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.57 % Allowed : 12.69 % Favored : 85.75 % 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: 0.29 (0.23), residues: 1474 helix: 1.03 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -1.73 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 342 HIS 0.007 0.001 HIS A 541 PHE 0.017 0.001 PHE B 471 TYR 0.010 0.001 TYR B 472 ARG 0.002 0.000 ARG B 436 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 613) hydrogen bonds : angle 3.93194 ( 1779) covalent geometry : bond 0.00227 (12368) covalent geometry : angle 0.52833 (16916) Misc. bond : bond 0.02087 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 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 147 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.288 Fit side-chains REVERT: A 130 GLN cc_start: 0.5327 (mm-40) cc_final: 0.4861 (pp30) REVERT: A 265 GLU cc_start: 0.8099 (pt0) cc_final: 0.7560 (tp30) REVERT: A 318 LEU cc_start: 0.5199 (OUTLIER) cc_final: 0.4639 (mp) REVERT: A 379 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7102 (m-80) REVERT: A 471 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7503 (p90) REVERT: B 130 GLN cc_start: 0.5348 (mm-40) cc_final: 0.4866 (pp30) REVERT: B 265 GLU cc_start: 0.8086 (pt0) cc_final: 0.7551 (tp30) REVERT: B 318 LEU cc_start: 0.5142 (OUTLIER) cc_final: 0.4582 (mp) REVERT: B 379 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7106 (m-80) REVERT: B 471 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7488 (p90) outliers start: 19 outliers final: 12 residues processed: 135 average time/residue: 0.2236 time to fit residues: 45.2119 Evaluate side-chains 141 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 318 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 605 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.107326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.085430 restraints weight = 15801.132| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.64 r_work: 0.2743 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12372 Z= 0.121 Angle : 0.562 12.009 16916 Z= 0.270 Chirality : 0.040 0.145 1808 Planarity : 0.004 0.041 2080 Dihedral : 6.505 73.278 1620 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.57 % Allowed : 12.77 % Favored : 85.67 % 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: 0.22 (0.23), residues: 1474 helix: 0.99 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -1.79 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 342 HIS 0.007 0.001 HIS A 541 PHE 0.022 0.001 PHE A 471 TYR 0.012 0.001 TYR B 472 ARG 0.003 0.000 ARG B 724 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 613) hydrogen bonds : angle 4.03281 ( 1779) covalent geometry : bond 0.00296 (12368) covalent geometry : angle 0.56172 (16916) Misc. bond : bond 0.03063 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 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 140 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.357 Fit side-chains REVERT: A 265 GLU cc_start: 0.8150 (pt0) cc_final: 0.7541 (tp30) REVERT: A 379 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7140 (m-80) REVERT: A 471 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7725 (p90) REVERT: B 265 GLU cc_start: 0.8145 (pt0) cc_final: 0.7533 (tp30) REVERT: B 379 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7143 (m-80) REVERT: B 471 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7717 (p90) outliers start: 19 outliers final: 15 residues processed: 130 average time/residue: 0.2267 time to fit residues: 43.9689 Evaluate side-chains 137 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 318 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 605 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 105 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.108311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.086424 restraints weight = 15790.107| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.64 r_work: 0.2777 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12372 Z= 0.107 Angle : 0.544 10.893 16916 Z= 0.265 Chirality : 0.039 0.141 1808 Planarity : 0.004 0.040 2080 Dihedral : 6.462 72.847 1620 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.57 % Allowed : 12.85 % Favored : 85.58 % 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: 0.32 (0.23), residues: 1474 helix: 1.06 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -1.73 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 342 HIS 0.007 0.001 HIS A 541 PHE 0.019 0.001 PHE A 471 TYR 0.010 0.001 TYR A 472 ARG 0.002 0.000 ARG B 436 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 613) hydrogen bonds : angle 3.99691 ( 1779) covalent geometry : bond 0.00255 (12368) covalent geometry : angle 0.54450 (16916) Misc. bond : bond 0.02552 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5821.43 seconds wall clock time: 100 minutes 24.54 seconds (6024.54 seconds total)