Starting phenix.real_space_refine on Thu Aug 6 07:19:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wyl_66368/08_2026/9wyl_66368.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wyl_66368/08_2026/9wyl_66368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wyl_66368/08_2026/9wyl_66368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wyl_66368/08_2026/9wyl_66368.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wyl_66368/08_2026/9wyl_66368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wyl_66368/08_2026/9wyl_66368.map" } resolution = 3.4 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= 0.001 sd= 0.041 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 8936 2.51 5 N 2276 2.21 5 O 2342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13612 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6718 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 812} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 6718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6718 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 812} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 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: 2.41, per 1000 atoms: 0.18 Number of scatterers: 13612 At special positions: 0 Unit cell: (162.64, 72.76, 119.84, 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 2342 8.00 N 2276 7.00 C 8936 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: 0.88 Conformation dependent library (CDL) restraints added in 460.2 milliseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3104 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 2 sheets defined 82.9% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 1 through 3 No H-bonds generated for 'chain 'A' and resid 1 through 3' Processing helix chain 'A' and resid 4 through 33 removed outlier: 3.554A pdb=" N GLY A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.633A pdb=" N LEU A 111 " --> pdb=" O TYR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 128 Processing helix chain 'A' and resid 142 through 161 removed outlier: 3.730A pdb=" N ALA A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 182 through 202 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 226 through 255 removed outlier: 3.501A pdb=" N VAL A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 255 " --> pdb=" O TRP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.635A pdb=" N THR A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE A 273 " --> pdb=" O PRO A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 273' Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 281 through 310 removed outlier: 4.428A pdb=" N TYR A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 355 removed outlier: 3.795A pdb=" N ALA A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Proline residue: A 352 - end of helix Processing helix chain 'A' and resid 362 through 390 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 412 through 440 removed outlier: 3.627A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 445 through 461 Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.927A pdb=" N GLY A 465 " --> pdb=" O TYR A 462 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 466 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 467' Processing helix chain 'A' and resid 473 through 491 removed outlier: 3.632A pdb=" N LEU A 487 " --> pdb=" O TRP A 483 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 508 removed outlier: 3.515A pdb=" N PHE A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.851A pdb=" N GLY A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 539 removed outlier: 3.624A pdb=" N PHE A 536 " --> pdb=" O PRO A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 565 removed outlier: 3.731A pdb=" N MET A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Proline residue: A 562 - end of helix removed outlier: 4.352A pdb=" N VAL A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 576 removed outlier: 4.361A pdb=" N GLU A 569 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.616A pdb=" N ASN A 585 " --> pdb=" O TRP A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 611 removed outlier: 3.556A pdb=" N PHE A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 4.244A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 654 removed outlier: 3.589A pdb=" N VAL A 628 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 681 Processing helix chain 'A' and resid 682 through 698 removed outlier: 3.558A pdb=" N ILE A 686 " --> pdb=" O SER A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 704 Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 710 through 720 Processing helix chain 'A' and resid 720 through 745 removed outlier: 4.686A pdb=" N VAL A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A 745 " --> pdb=" O GLY A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 759 removed outlier: 3.597A pdb=" N ASN A 752 " --> pdb=" O ASP A 748 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 Processing helix chain 'A' and resid 768 through 778 removed outlier: 3.989A pdb=" N VAL A 772 " --> pdb=" O ASN A 768 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 778 " --> pdb=" O ASP A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 788 removed outlier: 3.914A pdb=" N LYS A 788 " --> pdb=" O LEU A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 795 removed outlier: 3.766A pdb=" N GLU A 795 " --> pdb=" O PRO A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 827 Processing helix chain 'A' and resid 829 through 848 Processing helix chain 'A' and resid 849 through 852 Processing helix chain 'B' and resid 4 through 33 removed outlier: 3.549A pdb=" N GLY B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY B 27 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU B 28 " --> pdb=" O PHE B 24 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.592A pdb=" N LEU B 111 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 128 Processing helix chain 'B' and resid 142 through 161 removed outlier: 3.729A pdb=" N ALA B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 182 through 202 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 226 through 255 removed outlier: 3.596A pdb=" N VAL B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 255 " --> pdb=" O TRP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.761A pdb=" N THR B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE B 273 " --> pdb=" O PRO B 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 268 through 273' Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 282 through 310 removed outlier: 3.659A pdb=" N THR B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.536A pdb=" N GLN B 320 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 355 removed outlier: 3.810A pdb=" N ALA B 335 " --> pdb=" O HIS B 331 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 336 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Proline residue: B 352 - end of helix removed outlier: 3.845A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 390 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 412 through 440 removed outlier: 3.610A pdb=" N GLY B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Proline residue: B 436 - end of helix Processing helix chain 'B' and resid 445 through 461 Processing helix chain 'B' and resid 462 through 467 removed outlier: 3.834A pdb=" N GLY B 465 " --> pdb=" O TYR B 462 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 466 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE B 467 " --> pdb=" O ALA B 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 462 through 467' Processing helix chain 'B' and resid 473 through 491 removed outlier: 3.630A pdb=" N LEU B 487 " --> pdb=" O TRP B 483 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 489 " --> pdb=" O VAL B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 508 Processing helix chain 'B' and resid 512 through 532 removed outlier: 3.887A pdb=" N GLY B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 538 removed outlier: 3.607A pdb=" N PHE B 536 " --> pdb=" O PRO B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 565 removed outlier: 3.730A pdb=" N MET B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Proline residue: B 562 - end of helix removed outlier: 4.330A pdb=" N VAL B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 576 removed outlier: 4.435A pdb=" N GLU B 569 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.578A pdb=" N ASN B 585 " --> pdb=" O TRP B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 611 removed outlier: 3.565A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 621 removed outlier: 4.310A pdb=" N TYR B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 654 removed outlier: 3.574A pdb=" N VAL B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 681 Processing helix chain 'B' and resid 682 through 698 removed outlier: 3.552A pdb=" N ILE B 686 " --> pdb=" O SER B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 Processing helix chain 'B' and resid 704 through 709 Processing helix chain 'B' and resid 710 through 720 Processing helix chain 'B' and resid 720 through 744 removed outlier: 4.723A pdb=" N VAL B 726 " --> pdb=" O PHE B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 747 No H-bonds generated for 'chain 'B' and resid 745 through 747' Processing helix chain 'B' and resid 748 through 758 removed outlier: 3.723A pdb=" N ASN B 752 " --> pdb=" O ASP B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 766 removed outlier: 3.803A pdb=" N ILE B 763 " --> pdb=" O ASN B 759 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS B 765 " --> pdb=" O LYS B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 777 removed outlier: 4.269A pdb=" N VAL B 772 " --> pdb=" O ASN B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 788 removed outlier: 3.850A pdb=" N LYS B 788 " --> pdb=" O LEU B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 795 removed outlier: 3.878A pdb=" N GLU B 795 " --> pdb=" O PRO B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 827 Processing helix chain 'B' and resid 829 through 848 Processing helix chain 'B' and resid 849 through 852 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 7.094A pdb=" N VAL A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU A 39 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 141 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA A 41 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 removed outlier: 7.078A pdb=" N VAL B 40 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU B 39 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU B 141 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 41 " --> pdb=" O LEU B 141 " (cutoff:3.500A) 939 hydrogen bonds defined for protein. 2739 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: 1.63 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 5822 1.39 - 1.55: 8106 1.55 - 1.72: 0 1.72 - 1.88: 96 1.88 - 2.04: 16 Bond restraints: 14040 Sorted by residual: bond pdb=" NC HEM A 901 " pdb="FE HEM A 901 " ideal model delta sigma weight residual 2.080 2.016 0.064 7.00e-02 2.04e+02 8.49e-01 bond pdb=" NC HEM B 901 " pdb="FE HEM B 901 " ideal model delta sigma weight residual 2.080 2.016 0.064 7.00e-02 2.04e+02 8.36e-01 bond pdb=" N PRO B 394 " pdb=" CA PRO B 394 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.31e-02 5.83e+03 8.18e-01 bond pdb=" CB ARG A 808 " pdb=" CG ARG A 808 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.50e-01 bond pdb=" CB MET B 515 " pdb=" CG MET B 515 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.20e-01 ... (remaining 14035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 18986 2.53 - 5.07: 182 5.07 - 7.60: 11 7.60 - 10.13: 4 10.13 - 12.66: 5 Bond angle restraints: 19188 Sorted by residual: angle pdb=" N ILE A 221 " pdb=" CA ILE A 221 " pdb=" C ILE A 221 " ideal model delta sigma weight residual 112.29 108.62 3.67 9.40e-01 1.13e+00 1.53e+01 angle pdb=" CB MET A 515 " pdb=" CG MET A 515 " pdb=" SD MET A 515 " ideal model delta sigma weight residual 112.70 123.65 -10.95 3.00e+00 1.11e-01 1.33e+01 angle pdb=" CA MET A 804 " pdb=" CB MET A 804 " pdb=" CG MET A 804 " ideal model delta sigma weight residual 114.10 121.30 -7.20 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CB MET B 515 " pdb=" CG MET B 515 " pdb=" SD MET B 515 " ideal model delta sigma weight residual 112.70 122.42 -9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" CB MET A 477 " pdb=" CG MET A 477 " pdb=" SD MET A 477 " ideal model delta sigma weight residual 112.70 121.29 -8.59 3.00e+00 1.11e-01 8.20e+00 ... (remaining 19183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7349 17.90 - 35.80: 472 35.80 - 53.70: 87 53.70 - 71.59: 20 71.59 - 89.49: 16 Dihedral angle restraints: 7944 sinusoidal: 3078 harmonic: 4866 Sorted by residual: dihedral pdb=" CA VAL A 637 " pdb=" C VAL A 637 " pdb=" N TYR A 638 " pdb=" CA TYR A 638 " ideal model delta harmonic sigma weight residual 180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" C2D HEM A 901 " pdb=" C3D HEM A 901 " pdb=" CAD HEM A 901 " pdb=" CBD HEM A 901 " ideal model delta sinusoidal sigma weight residual 180.00 95.27 84.73 2 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" C2D HEM B 901 " pdb=" C3D HEM B 901 " pdb=" CAD HEM B 901 " pdb=" CBD HEM B 901 " ideal model delta sinusoidal sigma weight residual 180.00 95.40 84.60 2 2.00e+01 2.50e-03 1.19e+01 ... (remaining 7941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1229 0.025 - 0.051: 458 0.051 - 0.076: 236 0.076 - 0.101: 90 0.101 - 0.126: 29 Chirality restraints: 2042 Sorted by residual: chirality pdb=" CA ILE B 72 " pdb=" N ILE B 72 " pdb=" C ILE B 72 " pdb=" CB ILE B 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA ILE A 36 " pdb=" N ILE A 36 " pdb=" C ILE A 36 " pdb=" CB ILE A 36 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 2039 not shown) Planarity restraints: 2410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 601 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C MET B 601 " -0.035 2.00e-02 2.50e+03 pdb=" O MET B 601 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU B 602 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 601 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" C MET A 601 " 0.035 2.00e-02 2.50e+03 pdb=" O MET A 601 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 602 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 626 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO B 627 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 627 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 627 " 0.023 5.00e-02 4.00e+02 ... (remaining 2407 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 217 2.70 - 3.25: 13912 3.25 - 3.80: 22714 3.80 - 4.35: 27737 4.35 - 4.90: 47529 Nonbonded interactions: 112109 Sorted by model distance: nonbonded pdb=" NE2 HIS B 537 " pdb="FE FE B 903 " model vdw 2.145 2.340 nonbonded pdb=" NE2 HIS A 537 " pdb="FE FE A 903 " model vdw 2.160 2.340 nonbonded pdb=" NE2 HIS B 538 " pdb="FE FE B 903 " model vdw 2.203 2.340 nonbonded pdb=" NE2 HIS A 538 " pdb="FE FE A 903 " model vdw 2.217 2.340 nonbonded pdb=" O ARG A 187 " pdb=" OG1 THR A 190 " model vdw 2.234 3.040 ... (remaining 112104 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: 0.01 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: 6.520 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.230 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 : 0.004 0.183 14044 Z= 0.161 Angle : 0.631 12.665 19188 Z= 0.332 Chirality : 0.037 0.126 2042 Planarity : 0.004 0.041 2410 Dihedral : 13.150 89.493 4840 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.60 % Allowed : 3.87 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.61 (0.21), residues: 1700 helix: 2.41 (0.15), residues: 1194 sheet: None (None), residues: 0 loop : 0.11 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 808 TYR 0.011 0.001 TYR A 78 PHE 0.011 0.001 PHE B 807 TRP 0.017 0.001 TRP B 338 HIS 0.004 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (14040) covalent geometry : angle 0.63127 / 0.33 (19188) hydrogen bonds : bond 0.12139 / 8.48 ( 939) hydrogen bonds : angle 5.25357 / 3.91 ( 2739) Misc. bond : bond 0.14899 / 7.55 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8977 (mtm) cc_final: 0.8329 (mtm) REVERT: A 393 MET cc_start: 0.8620 (ttm) cc_final: 0.8385 (ttm) REVERT: B 67 MET cc_start: 0.8988 (mtm) cc_final: 0.8422 (mtm) REVERT: B 430 MET cc_start: 0.8912 (tpp) cc_final: 0.8466 (tpp) REVERT: B 678 MET cc_start: 0.8396 (tmm) cc_final: 0.8111 (tmm) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 0.0974 time to fit residues: 9.0398 Evaluate side-chains 57 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 656 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.064382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.044800 restraints weight = 83135.691| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 5.45 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.212 14044 Z= 0.137 Angle : 0.544 11.580 19188 Z= 0.260 Chirality : 0.037 0.132 2042 Planarity : 0.004 0.037 2410 Dihedral : 6.430 84.032 1890 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.97 % Allowed : 4.69 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.70 (0.21), residues: 1700 helix: 2.54 (0.15), residues: 1194 sheet: None (None), residues: 0 loop : -0.04 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 432 TYR 0.010 0.001 TYR A 638 PHE 0.014 0.001 PHE B 493 TRP 0.016 0.001 TRP B 338 HIS 0.006 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (14040) covalent geometry : angle 0.54436 / 0.26 (19188) hydrogen bonds : bond 0.04699 / 3.20 ( 939) hydrogen bonds : angle 4.48607 / 3.29 ( 2739) Misc. bond : bond 0.16176 / 8.23 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8976 (mtm) cc_final: 0.8353 (mtm) REVERT: A 393 MET cc_start: 0.8618 (ttm) cc_final: 0.8348 (ttm) REVERT: B 67 MET cc_start: 0.9018 (mtm) cc_final: 0.8459 (mtm) REVERT: B 664 MET cc_start: 0.9502 (mmm) cc_final: 0.9260 (tpp) outliers start: 13 outliers final: 5 residues processed: 62 average time/residue: 0.0896 time to fit residues: 9.0234 Evaluate side-chains 56 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 460 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.064394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.044676 restraints weight = 83691.908| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 5.48 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.225 14044 Z= 0.130 Angle : 0.536 13.135 19188 Z= 0.251 Chirality : 0.037 0.144 2042 Planarity : 0.004 0.035 2410 Dihedral : 6.199 84.245 1882 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.34 % Allowed : 4.99 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.76 (0.21), residues: 1700 helix: 2.58 (0.15), residues: 1196 sheet: None (None), residues: 0 loop : -0.04 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 432 TYR 0.010 0.001 TYR A 638 PHE 0.012 0.001 PHE A 493 TRP 0.016 0.001 TRP B 338 HIS 0.005 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (14040) covalent geometry : angle 0.53630 / 0.25 (19188) hydrogen bonds : bond 0.04342 / 2.95 ( 939) hydrogen bonds : angle 4.31404 / 3.17 ( 2739) Misc. bond : bond 0.16131 / 8.24 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8935 (mtm) cc_final: 0.8278 (mtm) REVERT: A 393 MET cc_start: 0.8647 (ttm) cc_final: 0.8383 (ttm) REVERT: B 67 MET cc_start: 0.8975 (mtm) cc_final: 0.8462 (mtm) REVERT: B 664 MET cc_start: 0.9492 (mmm) cc_final: 0.9286 (tpp) outliers start: 18 outliers final: 10 residues processed: 67 average time/residue: 0.0936 time to fit residues: 9.8437 Evaluate side-chains 59 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 620 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 48 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 115 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 168 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.0000 chunk 6 optimal weight: 3.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.064244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.045054 restraints weight = 84068.964| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 5.13 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.193 14044 Z= 0.106 Angle : 0.507 11.508 19188 Z= 0.238 Chirality : 0.036 0.120 2042 Planarity : 0.003 0.033 2410 Dihedral : 6.157 84.899 1882 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.71 % Allowed : 4.91 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.21), residues: 1700 helix: 2.63 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : 0.07 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 432 TYR 0.010 0.001 TYR B 638 PHE 0.011 0.001 PHE A 609 TRP 0.016 0.001 TRP B 338 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (14040) covalent geometry : angle 0.50668 / 0.24 (19188) hydrogen bonds : bond 0.03954 / 2.69 ( 939) hydrogen bonds : angle 4.18347 / 3.07 ( 2739) Misc. bond : bond 0.13786 / 7.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8881 (mtm) cc_final: 0.8259 (mtm) REVERT: A 393 MET cc_start: 0.8667 (ttm) cc_final: 0.8405 (ttm) REVERT: B 67 MET cc_start: 0.8922 (mtm) cc_final: 0.8379 (mtm) REVERT: B 393 MET cc_start: 0.8770 (tpp) cc_final: 0.8528 (tpp) outliers start: 23 outliers final: 13 residues processed: 73 average time/residue: 0.0921 time to fit residues: 10.7074 Evaluate side-chains 64 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 620 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.064034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.044476 restraints weight = 84932.477| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 5.48 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.220 14044 Z= 0.124 Angle : 0.535 13.370 19188 Z= 0.245 Chirality : 0.036 0.120 2042 Planarity : 0.003 0.033 2410 Dihedral : 6.151 84.614 1882 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.34 % Allowed : 5.28 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.91 (0.21), residues: 1700 helix: 2.65 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : 0.13 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 432 TYR 0.010 0.001 TYR A 638 PHE 0.020 0.001 PHE B 493 TRP 0.016 0.001 TRP B 338 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (14040) covalent geometry : angle 0.53451 / 0.25 (19188) hydrogen bonds : bond 0.03951 / 2.69 ( 939) hydrogen bonds : angle 4.16548 / 3.06 ( 2739) Misc. bond : bond 0.15676 / 8.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8912 (mtm) cc_final: 0.8298 (mtm) REVERT: A 393 MET cc_start: 0.8633 (ttm) cc_final: 0.8381 (ttm) REVERT: A 493 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8209 (m-80) REVERT: B 67 MET cc_start: 0.8967 (mtm) cc_final: 0.8437 (mtm) REVERT: B 393 MET cc_start: 0.8746 (tpp) cc_final: 0.8492 (tpp) outliers start: 18 outliers final: 12 residues processed: 67 average time/residue: 0.0930 time to fit residues: 10.1092 Evaluate side-chains 62 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 620 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 35 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 GLN ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS B 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.062696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.043067 restraints weight = 84940.770| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 5.42 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.327 14044 Z= 0.252 Angle : 0.668 18.384 19188 Z= 0.302 Chirality : 0.039 0.126 2042 Planarity : 0.004 0.034 2410 Dihedral : 6.316 81.634 1882 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.56 % Allowed : 5.73 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.68 (0.21), residues: 1700 helix: 2.44 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : 0.13 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 780 TYR 0.013 0.001 TYR B 78 PHE 0.020 0.002 PHE A 811 TRP 0.016 0.001 TRP B 338 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.25 (14040) covalent geometry : angle 0.66796 / 0.30 (19188) hydrogen bonds : bond 0.04813 / 3.27 ( 939) hydrogen bonds : angle 4.38627 / 3.22 ( 2739) Misc. bond : bond 0.24088 / 12.29 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.9104 (mtm) cc_final: 0.8519 (mtm) REVERT: A 393 MET cc_start: 0.8624 (ttm) cc_final: 0.8342 (ttm) REVERT: A 493 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8342 (m-80) REVERT: B 28 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: B 67 MET cc_start: 0.9120 (mtm) cc_final: 0.8596 (mtm) REVERT: B 393 MET cc_start: 0.8849 (tpp) cc_final: 0.8517 (tpp) outliers start: 21 outliers final: 14 residues processed: 69 average time/residue: 0.0788 time to fit residues: 8.8496 Evaluate side-chains 67 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 620 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 74 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 43 optimal weight: 0.0020 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 30.0000 chunk 150 optimal weight: 0.9980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.063722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.044057 restraints weight = 83398.508| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 5.65 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 14044 Z= 0.107 Angle : 0.524 11.187 19188 Z= 0.245 Chirality : 0.036 0.123 2042 Planarity : 0.003 0.033 2410 Dihedral : 6.234 83.114 1882 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.26 % Allowed : 6.32 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.99 (0.21), residues: 1700 helix: 2.68 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : 0.21 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 280 TYR 0.010 0.001 TYR B 638 PHE 0.011 0.001 PHE A 609 TRP 0.015 0.001 TRP B 338 HIS 0.006 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (14040) covalent geometry : angle 0.52400 / 0.24 (19188) hydrogen bonds : bond 0.03981 / 2.71 ( 939) hydrogen bonds : angle 4.13215 / 3.04 ( 2739) Misc. bond : bond 0.14919 / 7.58 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8972 (mtm) cc_final: 0.8365 (mtm) REVERT: A 393 MET cc_start: 0.8581 (ttm) cc_final: 0.8288 (ttm) REVERT: A 493 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: B 67 MET cc_start: 0.9008 (mtm) cc_final: 0.8482 (mtm) REVERT: B 393 MET cc_start: 0.8710 (tpp) cc_final: 0.8454 (tpp) REVERT: B 493 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8275 (m-80) outliers start: 17 outliers final: 11 residues processed: 66 average time/residue: 0.0943 time to fit residues: 10.0424 Evaluate side-chains 63 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 620 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 164 optimal weight: 0.1980 chunk 88 optimal weight: 0.5980 chunk 136 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.064018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.044460 restraints weight = 83701.575| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 5.55 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.186 14044 Z= 0.108 Angle : 0.533 12.572 19188 Z= 0.245 Chirality : 0.036 0.143 2042 Planarity : 0.003 0.033 2410 Dihedral : 6.084 83.668 1880 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.49 % Allowed : 6.47 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.21), residues: 1700 helix: 2.71 (0.15), residues: 1206 sheet: None (None), residues: 0 loop : 0.20 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 514 TYR 0.009 0.001 TYR B 638 PHE 0.042 0.001 PHE A 811 TRP 0.015 0.001 TRP B 338 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (14040) covalent geometry : angle 0.53348 / 0.24 (19188) hydrogen bonds : bond 0.03815 / 2.60 ( 939) hydrogen bonds : angle 4.09794 / 3.02 ( 2739) Misc. bond : bond 0.14063 / 7.15 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8900 (mtm) cc_final: 0.8335 (mtm) REVERT: A 393 MET cc_start: 0.8580 (ttm) cc_final: 0.8300 (ttm) REVERT: A 493 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: B 67 MET cc_start: 0.8974 (mtm) cc_final: 0.8489 (mtm) REVERT: B 393 MET cc_start: 0.8690 (tpp) cc_final: 0.8457 (tpp) REVERT: B 493 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8239 (m-80) REVERT: B 664 MET cc_start: 0.9380 (mmm) cc_final: 0.9149 (tpp) outliers start: 20 outliers final: 14 residues processed: 69 average time/residue: 0.0922 time to fit residues: 10.4375 Evaluate side-chains 68 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 620 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 42 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.062469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.042670 restraints weight = 84875.053| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 5.53 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.331 14044 Z= 0.268 Angle : 0.690 18.493 19188 Z= 0.311 Chirality : 0.040 0.145 2042 Planarity : 0.004 0.034 2410 Dihedral : 6.278 80.761 1880 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.56 % Allowed : 6.47 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.68 (0.21), residues: 1700 helix: 2.44 (0.15), residues: 1206 sheet: None (None), residues: 0 loop : 0.14 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 514 TYR 0.016 0.002 TYR B 78 PHE 0.033 0.002 PHE A 811 TRP 0.016 0.001 TRP B 338 HIS 0.005 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.27 (14040) covalent geometry : angle 0.68957 / 0.31 (19188) hydrogen bonds : bond 0.04823 / 3.27 ( 939) hydrogen bonds : angle 4.37762 / 3.22 ( 2739) Misc. bond : bond 0.24717 / 12.60 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.9128 (mtm) cc_final: 0.8557 (mtm) REVERT: A 393 MET cc_start: 0.8580 (ttm) cc_final: 0.8275 (ttm) REVERT: A 493 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8434 (m-10) REVERT: B 67 MET cc_start: 0.9134 (mtm) cc_final: 0.8616 (mtm) REVERT: B 393 MET cc_start: 0.8817 (tpp) cc_final: 0.8552 (tpp) outliers start: 21 outliers final: 15 residues processed: 71 average time/residue: 0.0999 time to fit residues: 11.5857 Evaluate side-chains 68 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 620 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 108 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.063376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.043812 restraints weight = 84365.072| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 5.60 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.222 14044 Z= 0.120 Angle : 0.548 12.619 19188 Z= 0.253 Chirality : 0.037 0.121 2042 Planarity : 0.003 0.033 2410 Dihedral : 6.060 81.996 1878 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.12 % Allowed : 6.92 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.97 (0.21), residues: 1700 helix: 2.67 (0.15), residues: 1202 sheet: None (None), residues: 0 loop : 0.20 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 432 TYR 0.010 0.001 TYR A 638 PHE 0.028 0.001 PHE A 811 TRP 0.015 0.001 TRP B 338 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (14040) covalent geometry : angle 0.54828 / 0.25 (19188) hydrogen bonds : bond 0.04124 / 2.81 ( 939) hydrogen bonds : angle 4.14713 / 3.06 ( 2739) Misc. bond : bond 0.16939 / 8.62 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.439 Fit side-chains REVERT: A 67 MET cc_start: 0.8986 (mtm) cc_final: 0.8408 (mtm) REVERT: A 393 MET cc_start: 0.8537 (ttm) cc_final: 0.8218 (ttm) REVERT: A 493 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8341 (m-10) REVERT: A 664 MET cc_start: 0.9394 (mmm) cc_final: 0.9101 (tpp) REVERT: B 67 MET cc_start: 0.9018 (mtm) cc_final: 0.8509 (mtm) REVERT: B 393 MET cc_start: 0.8718 (tpp) cc_final: 0.8476 (tpp) REVERT: B 664 MET cc_start: 0.9381 (mmm) cc_final: 0.8995 (tpp) outliers start: 15 outliers final: 14 residues processed: 68 average time/residue: 0.0943 time to fit residues: 10.3699 Evaluate side-chains 66 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 620 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 7 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 152 optimal weight: 0.0870 chunk 125 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.063408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.043850 restraints weight = 85253.869| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 5.80 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.214 14044 Z= 0.126 Angle : 0.564 13.404 19188 Z= 0.257 Chirality : 0.037 0.118 2042 Planarity : 0.003 0.033 2410 Dihedral : 6.003 81.902 1878 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.19 % Allowed : 6.99 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.21), residues: 1700 helix: 2.71 (0.15), residues: 1202 sheet: None (None), residues: 0 loop : 0.20 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 168 TYR 0.010 0.001 TYR A 78 PHE 0.025 0.001 PHE A 811 TRP 0.016 0.001 TRP B 338 HIS 0.006 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (14040) covalent geometry : angle 0.56378 / 0.26 (19188) hydrogen bonds : bond 0.04016 / 2.73 ( 939) hydrogen bonds : angle 4.11357 / 3.03 ( 2739) Misc. bond : bond 0.16270 / 8.28 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2356.20 seconds wall clock time: 41 minutes 14.88 seconds (2474.88 seconds total)