Starting phenix.real_space_refine on Wed Mar 4 07:56:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l3h_0822/03_2026/6l3h_0822.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l3h_0822/03_2026/6l3h_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_0822/03_2026/6l3h_0822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l3h_0822/03_2026/6l3h_0822.map" model { file = "/net/cci-nas-00/data/ceres_data/6l3h_0822/03_2026/6l3h_0822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l3h_0822/03_2026/6l3h_0822.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.20, per 1000 atoms: 0.18 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: 0.92 Conformation dependent library (CDL) restraints added in 545.1 milliseconds 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: 0.35 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: 1.90 Time building geometry restraints manager: 1.27 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: 0.02 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: 0.740 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.670 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.270 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.60 (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 ARG 0.002 0.000 ARG A 332 TYR 0.015 0.002 TYR A 328 PHE 0.038 0.002 PHE A 471 TRP 0.022 0.002 TRP A 342 HIS 0.008 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00725 (12368) covalent geometry : angle 0.76745 (16916) hydrogen bonds : bond 0.25183 ( 613) hydrogen bonds : angle 8.24167 ( 1779) 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 : 0.442 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: 0.1216 time to fit residues: 20.2625 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 : 0.393 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3117 r_free = 0.3117 target = 0.104186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.082892 restraints weight = 16082.584| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.60 r_work: 0.2688 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12372 Z= 0.134 Angle : 0.602 7.637 16916 Z= 0.313 Chirality : 0.040 0.155 1808 Planarity : 0.005 0.050 2080 Dihedral : 7.460 73.600 1624 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.88 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.20), residues: 1474 helix: -1.43 (0.15), residues: 1018 sheet: None (None), residues: 0 loop : -2.75 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 516 TYR 0.013 0.001 TYR A 510 PHE 0.022 0.001 PHE A 471 TRP 0.018 0.001 TRP A 342 HIS 0.005 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00298 (12368) covalent geometry : angle 0.60231 (16916) hydrogen bonds : bond 0.05846 ( 613) hydrogen bonds : angle 4.99960 ( 1779) Misc. bond : bond 0.03144 ( 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 120 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.369 Fit side-chains REVERT: A 365 LYS cc_start: 0.5313 (mttt) cc_final: 0.4517 (mmmt) REVERT: B 682 MET cc_start: 0.8879 (ptt) cc_final: 0.8661 (ptp) outliers start: 13 outliers final: 6 residues processed: 113 average time/residue: 0.0926 time to fit residues: 16.0314 Evaluate side-chains 99 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 133 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 18 optimal weight: 0.1980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3098 r_free = 0.3098 target = 0.102750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.081150 restraints weight = 16193.695| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 1.61 r_work: 0.2678 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12372 Z= 0.154 Angle : 0.621 12.940 16916 Z= 0.304 Chirality : 0.042 0.158 1808 Planarity : 0.004 0.043 2080 Dihedral : 7.320 74.699 1624 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.74 % Allowed : 10.21 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.21), residues: 1474 helix: -0.57 (0.16), residues: 1012 sheet: None (None), residues: 0 loop : -2.54 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 516 TYR 0.012 0.001 TYR B 328 PHE 0.028 0.001 PHE A 471 TRP 0.018 0.001 TRP A 342 HIS 0.006 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00376 (12368) covalent geometry : angle 0.62087 (16916) hydrogen bonds : bond 0.05198 ( 613) hydrogen bonds : angle 4.61126 ( 1779) Misc. bond : bond 0.03351 ( 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 114 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.424 Fit side-chains REVERT: A 365 LYS cc_start: 0.5249 (mttt) cc_final: 0.4418 (mmmt) REVERT: A 715 GLU cc_start: 0.8425 (tp30) cc_final: 0.8154 (tp30) REVERT: A 728 ASP cc_start: 0.7408 (m-30) cc_final: 0.7173 (m-30) REVERT: B 715 GLU cc_start: 0.8455 (tp30) cc_final: 0.8181 (tp30) outliers start: 9 outliers final: 7 residues processed: 109 average time/residue: 0.0897 time to fit residues: 15.1713 Evaluate side-chains 106 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 262 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 84 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 chunk 49 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.104753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.082917 restraints weight = 15946.062| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.63 r_work: 0.2702 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12372 Z= 0.122 Angle : 0.565 11.430 16916 Z= 0.280 Chirality : 0.040 0.149 1808 Planarity : 0.004 0.042 2080 Dihedral : 6.850 73.638 1620 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.15 % Allowed : 11.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.22), residues: 1474 helix: -0.08 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -2.26 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 516 TYR 0.012 0.001 TYR B 472 PHE 0.022 0.001 PHE A 471 TRP 0.017 0.001 TRP A 342 HIS 0.007 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00293 (12368) covalent geometry : angle 0.56506 (16916) hydrogen bonds : bond 0.04403 ( 613) hydrogen bonds : angle 4.35235 ( 1779) Misc. bond : bond 0.02508 ( 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 115 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.353 Fit side-chains REVERT: A 265 GLU cc_start: 0.8134 (pt0) cc_final: 0.7435 (tp30) REVERT: A 471 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7860 (p90) REVERT: A 715 GLU cc_start: 0.8348 (tp30) cc_final: 0.8063 (tp30) REVERT: B 265 GLU cc_start: 0.8156 (pt0) cc_final: 0.7490 (tp30) REVERT: B 471 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7833 (p90) REVERT: B 715 GLU cc_start: 0.8347 (tp30) cc_final: 0.8069 (tp30) outliers start: 14 outliers final: 7 residues processed: 109 average time/residue: 0.0846 time to fit residues: 14.4179 Evaluate side-chains 108 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 262 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 605 MET 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 140 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 113 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 741 GLN 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 = 0.110358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.088584 restraints weight = 15640.630| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.64 r_work: 0.2757 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1883 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= 0.110 Angle : 0.555 10.741 16916 Z= 0.271 Chirality : 0.040 0.147 1808 Planarity : 0.004 0.043 2080 Dihedral : 6.730 73.731 1620 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.81 % Allowed : 10.46 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.22), residues: 1474 helix: 0.23 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -2.08 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 436 TYR 0.011 0.001 TYR A 472 PHE 0.020 0.001 PHE A 471 TRP 0.017 0.001 TRP A 342 HIS 0.007 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00258 (12368) covalent geometry : angle 0.55452 (16916) hydrogen bonds : bond 0.04045 ( 613) hydrogen bonds : angle 4.21541 ( 1779) Misc. bond : bond 0.02675 ( 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: 22 poor density : 108 time to evaluate : 0.376 Fit side-chains REVERT: A 265 GLU cc_start: 0.8158 (pt0) cc_final: 0.7503 (tp30) REVERT: A 471 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7867 (p90) REVERT: A 715 GLU cc_start: 0.8349 (tp30) cc_final: 0.8070 (tp30) REVERT: B 265 GLU cc_start: 0.8126 (pt0) cc_final: 0.7523 (tp30) REVERT: B 471 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7842 (p90) REVERT: B 715 GLU cc_start: 0.8375 (tp30) cc_final: 0.8098 (tp30) outliers start: 22 outliers final: 15 residues processed: 121 average time/residue: 0.0816 time to fit residues: 15.7658 Evaluate side-chains 121 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU 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 605 MET Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain B residue 98 LEU 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 553 MET Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 665 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 77 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 0.0070 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.109786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.088088 restraints weight = 15779.061| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.61 r_work: 0.2801 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2183 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 : 0.521 8.727 16916 Z= 0.260 Chirality : 0.039 0.139 1808 Planarity : 0.004 0.042 2080 Dihedral : 6.537 73.438 1620 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.48 % Allowed : 11.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.23), residues: 1474 helix: 0.52 (0.17), residues: 1018 sheet: None (None), residues: 0 loop : -2.00 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 436 TYR 0.009 0.001 TYR B 510 PHE 0.016 0.001 PHE A 471 TRP 0.017 0.001 TRP A 342 HIS 0.007 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00222 (12368) covalent geometry : angle 0.52133 (16916) hydrogen bonds : bond 0.03478 ( 613) hydrogen bonds : angle 4.04353 ( 1779) Misc. bond : bond 0.01947 ( 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 143 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.448 Fit side-chains REVERT: A 265 GLU cc_start: 0.8117 (pt0) cc_final: 0.7490 (tp30) REVERT: A 471 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7600 (p90) REVERT: A 496 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7458 (t80) REVERT: A 715 GLU cc_start: 0.8391 (tp30) cc_final: 0.8151 (tp30) REVERT: B 265 GLU cc_start: 0.8119 (pt0) cc_final: 0.7549 (tp30) REVERT: B 471 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7586 (p90) REVERT: B 496 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7460 (t80) REVERT: B 715 GLU cc_start: 0.8390 (tp30) cc_final: 0.8154 (tp30) outliers start: 18 outliers final: 12 residues processed: 137 average time/residue: 0.0880 time to fit residues: 18.5933 Evaluate side-chains 129 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 A residue 605 MET Chi-restraints excluded: chain A residue 665 ASP 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 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 110 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3168 r_free = 0.3168 target = 0.108642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.086896 restraints weight = 15681.989| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.63 r_work: 0.2778 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12372 Z= 0.103 Angle : 0.535 10.966 16916 Z= 0.261 Chirality : 0.039 0.142 1808 Planarity : 0.004 0.042 2080 Dihedral : 6.531 73.413 1620 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.57 % Allowed : 12.93 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.23), residues: 1474 helix: 0.72 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -1.89 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 436 TYR 0.010 0.001 TYR B 472 PHE 0.019 0.001 PHE B 471 TRP 0.015 0.001 TRP A 342 HIS 0.007 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00242 (12368) covalent geometry : angle 0.53525 (16916) hydrogen bonds : bond 0.03637 ( 613) hydrogen bonds : angle 4.02442 ( 1779) Misc. bond : bond 0.02901 ( 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 142 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.403 Fit side-chains REVERT: A 5 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6875 (tptt) REVERT: A 265 GLU cc_start: 0.8103 (pt0) cc_final: 0.7494 (tp30) REVERT: A 471 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7667 (p90) REVERT: A 496 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7350 (t80) REVERT: A 715 GLU cc_start: 0.8396 (tp30) cc_final: 0.8158 (tp30) REVERT: B 265 GLU cc_start: 0.8134 (pt0) cc_final: 0.7489 (tp30) REVERT: B 471 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7654 (p90) REVERT: B 496 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7332 (t80) REVERT: B 624 ILE cc_start: 0.8314 (mm) cc_final: 0.7958 (mt) REVERT: B 715 GLU cc_start: 0.8393 (tp30) cc_final: 0.8134 (tp30) outliers start: 19 outliers final: 11 residues processed: 134 average time/residue: 0.0927 time to fit residues: 18.8567 Evaluate side-chains 139 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 24 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.0870 chunk 133 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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 = 0.3140 r_free = 0.3140 target = 0.106487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.084603 restraints weight = 15814.276| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.63 r_work: 0.2753 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12372 Z= 0.144 Angle : 0.579 12.379 16916 Z= 0.280 Chirality : 0.041 0.154 1808 Planarity : 0.004 0.042 2080 Dihedral : 6.628 73.180 1620 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.89 % Allowed : 12.85 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.23), residues: 1474 helix: 0.69 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -1.95 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 436 TYR 0.013 0.001 TYR B 472 PHE 0.026 0.001 PHE A 471 TRP 0.013 0.001 TRP A 342 HIS 0.007 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00357 (12368) covalent geometry : angle 0.57947 (16916) hydrogen bonds : bond 0.04267 ( 613) hydrogen bonds : angle 4.15130 ( 1779) Misc. bond : bond 0.04088 ( 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 137 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.386 Fit side-chains REVERT: A 5 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6908 (tptt) REVERT: A 265 GLU cc_start: 0.8130 (pt0) cc_final: 0.7497 (tp30) REVERT: A 379 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: A 471 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7889 (p90) REVERT: A 583 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8243 (mp) REVERT: A 715 GLU cc_start: 0.8386 (tp30) cc_final: 0.8117 (tp30) REVERT: B 5 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6874 (tptt) REVERT: B 265 GLU cc_start: 0.8149 (pt0) cc_final: 0.7491 (tp30) REVERT: B 471 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7935 (p90) REVERT: B 563 GLU cc_start: 0.8366 (tt0) cc_final: 0.8165 (tt0) outliers start: 23 outliers final: 14 residues processed: 125 average time/residue: 0.0905 time to fit residues: 17.4876 Evaluate side-chains 132 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS 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 437 CYS Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain B residue 5 LYS 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 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 89 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 132 optimal weight: 0.2980 chunk 13 optimal weight: 0.0970 chunk 147 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.108801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.086992 restraints weight = 15779.840| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.64 r_work: 0.2785 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12372 Z= 0.099 Angle : 0.522 8.251 16916 Z= 0.259 Chirality : 0.039 0.137 1808 Planarity : 0.004 0.042 2080 Dihedral : 6.490 73.461 1620 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.65 % Allowed : 13.10 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.23), residues: 1474 helix: 0.92 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -1.81 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 436 TYR 0.009 0.001 TYR B 472 PHE 0.016 0.001 PHE B 471 TRP 0.017 0.001 TRP B 342 HIS 0.007 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00231 (12368) covalent geometry : angle 0.52162 (16916) hydrogen bonds : bond 0.03471 ( 613) hydrogen bonds : angle 4.00564 ( 1779) Misc. bond : bond 0.02127 ( 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: 20 poor density : 127 time to evaluate : 0.429 Fit side-chains REVERT: A 265 GLU cc_start: 0.8098 (pt0) cc_final: 0.7494 (tp30) REVERT: A 379 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: A 471 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7606 (p90) REVERT: A 583 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8198 (mp) REVERT: B 5 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6818 (tptt) REVERT: B 265 GLU cc_start: 0.8135 (pt0) cc_final: 0.7551 (tp30) REVERT: B 379 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7114 (m-80) REVERT: B 471 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7599 (p90) REVERT: B 496 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7348 (t80) outliers start: 20 outliers final: 13 residues processed: 137 average time/residue: 0.0932 time to fit residues: 19.3781 Evaluate side-chains 143 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 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 437 CYS Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain B residue 5 LYS 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 437 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 46 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 581 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.086810 restraints weight = 15795.520| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.65 r_work: 0.2792 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12372 Z= 0.100 Angle : 0.532 10.025 16916 Z= 0.259 Chirality : 0.039 0.139 1808 Planarity : 0.004 0.041 2080 Dihedral : 6.483 73.694 1620 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.57 % Allowed : 13.10 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.23), residues: 1474 helix: 1.01 (0.17), residues: 1022 sheet: None (None), residues: 0 loop : -1.73 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 436 TYR 0.010 0.001 TYR B 472 PHE 0.018 0.001 PHE A 471 TRP 0.016 0.001 TRP B 342 HIS 0.007 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00235 (12368) covalent geometry : angle 0.53166 (16916) hydrogen bonds : bond 0.03507 ( 613) hydrogen bonds : angle 3.99984 ( 1779) Misc. bond : bond 0.02710 ( 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 148 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.413 Fit side-chains REVERT: A 5 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6888 (tptt) REVERT: A 265 GLU cc_start: 0.8112 (pt0) cc_final: 0.7515 (tp30) REVERT: A 379 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7180 (m-80) REVERT: A 471 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7547 (p90) REVERT: A 583 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8213 (mp) REVERT: B 5 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6841 (tptt) REVERT: B 265 GLU cc_start: 0.8134 (pt0) cc_final: 0.7544 (tp30) REVERT: B 379 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: B 471 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7542 (p90) outliers start: 19 outliers final: 12 residues processed: 136 average time/residue: 0.0917 time to fit residues: 18.9011 Evaluate side-chains 145 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS 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 583 LEU Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain B residue 5 LYS 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 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 137 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.106439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.084492 restraints weight = 15833.018| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.64 r_work: 0.2749 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12372 Z= 0.128 Angle : 0.569 11.842 16916 Z= 0.275 Chirality : 0.041 0.149 1808 Planarity : 0.004 0.042 2080 Dihedral : 6.561 73.136 1620 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.81 % Allowed : 13.10 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1474 helix: 0.95 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -1.81 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 436 TYR 0.011 0.001 TYR A 472 PHE 0.024 0.001 PHE B 471 TRP 0.013 0.001 TRP B 342 HIS 0.007 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00314 (12368) covalent geometry : angle 0.56937 (16916) hydrogen bonds : bond 0.04125 ( 613) hydrogen bonds : angle 4.10279 ( 1779) Misc. bond : bond 0.04121 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2495.24 seconds wall clock time: 43 minutes 26.28 seconds (2606.28 seconds total)