Starting phenix.real_space_refine on Tue Jun 17 09:11:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnm_26014/06_2025/7tnm_26014.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnm_26014/06_2025/7tnm_26014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tnm_26014/06_2025/7tnm_26014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnm_26014/06_2025/7tnm_26014.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnm_26014/06_2025/7tnm_26014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnm_26014/06_2025/7tnm_26014.cif" } resolution = 4.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12570 2.51 5 N 3144 2.21 5 O 3594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19448 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "B" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4835 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "C" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "D" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4835 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.61, per 1000 atoms: 0.60 Number of scatterers: 19448 At special positions: 0 Unit cell: (122.01, 117.03, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 136 16.00 O 3594 8.00 N 3144 7.00 C 12570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 2.3 seconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 56.4% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.751A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 Processing helix chain 'A' and resid 565 through 569 removed outlier: 4.130A pdb=" N ASN A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 569' Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.685A pdb=" N SER A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 770 Processing helix chain 'A' and resid 792 through 820 removed outlier: 3.639A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1028 Processing helix chain 'A' and resid 1091 through 1103 Processing helix chain 'A' and resid 1104 through 1123 Processing helix chain 'A' and resid 1132 through 1161 Processing helix chain 'A' and resid 1176 through 1209 Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.531A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 489 removed outlier: 3.715A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 545 Processing helix chain 'B' and resid 564 through 568 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 617 Processing helix chain 'B' and resid 620 through 624 Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 769 Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.588A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1029 Processing helix chain 'B' and resid 1039 through 1043 Processing helix chain 'B' and resid 1091 through 1103 removed outlier: 3.538A pdb=" N SER B1103 " --> pdb=" O ALA B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1123 Processing helix chain 'B' and resid 1132 through 1159 Processing helix chain 'B' and resid 1176 through 1209 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.751A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 488 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 545 Processing helix chain 'C' and resid 565 through 569 removed outlier: 4.131A pdb=" N ASN C 569 " --> pdb=" O SER C 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 565 through 569' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 625 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.685A pdb=" N SER C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 770 Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.639A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1028 Processing helix chain 'C' and resid 1091 through 1103 Processing helix chain 'C' and resid 1104 through 1123 Processing helix chain 'C' and resid 1132 through 1161 Processing helix chain 'C' and resid 1176 through 1209 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.531A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 489 removed outlier: 3.714A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'D' and resid 564 through 568 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 617 Processing helix chain 'D' and resid 620 through 624 Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 769 removed outlier: 3.501A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.588A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1029 Processing helix chain 'D' and resid 1039 through 1043 Processing helix chain 'D' and resid 1091 through 1103 removed outlier: 3.538A pdb=" N SER D1103 " --> pdb=" O ALA D1099 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1123 Processing helix chain 'D' and resid 1132 through 1159 Processing helix chain 'D' and resid 1176 through 1209 Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 498 removed outlier: 4.833A pdb=" N PHE A 491 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR A 736 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS A 493 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE A 734 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR A 732 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER A 497 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS A 730 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 702 through 705 removed outlier: 3.613A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1058 through 1060 Processing sheet with id=AA6, first strand: chain 'B' and resid 395 through 399 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.631A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 682 through 683 removed outlier: 7.658A pdb=" N VAL B 683 " --> pdb=" O TYR B 647 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR B 649 " --> pdb=" O VAL B 683 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N LEU B 650 " --> pdb=" O GLU B 705 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 682 through 683 removed outlier: 7.658A pdb=" N VAL B 683 " --> pdb=" O TYR B 647 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR B 649 " --> pdb=" O VAL B 683 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N LEU B 650 " --> pdb=" O GLU B 705 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1056 through 1060 Processing sheet with id=AB3, first strand: chain 'B' and resid 1064 through 1066 Processing sheet with id=AB4, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AB5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'C' and resid 489 through 498 removed outlier: 4.833A pdb=" N PHE C 491 " --> pdb=" O THR C 736 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR C 736 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS C 493 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE C 734 " --> pdb=" O LYS C 493 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 702 through 705 removed outlier: 3.612A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1058 through 1060 Processing sheet with id=AB9, first strand: chain 'D' and resid 395 through 399 Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.630A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 682 through 683 removed outlier: 7.659A pdb=" N VAL D 683 " --> pdb=" O TYR D 647 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 649 " --> pdb=" O VAL D 683 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N LEU D 650 " --> pdb=" O GLU D 705 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 682 through 683 removed outlier: 7.659A pdb=" N VAL D 683 " --> pdb=" O TYR D 647 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 649 " --> pdb=" O VAL D 683 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N LEU D 650 " --> pdb=" O GLU D 705 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1056 through 1060 Processing sheet with id=AC6, first strand: chain 'D' and resid 1064 through 1066 1117 hydrogen bonds defined for protein. 3243 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: 6.00 Time building geometry restraints manager: 5.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5439 1.34 - 1.46: 4181 1.46 - 1.58: 10034 1.58 - 1.70: 8 1.70 - 1.82: 220 Bond restraints: 19882 Sorted by residual: bond pdb=" N THR D1049 " pdb=" CA THR D1049 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 6.99e+00 bond pdb=" N THR B1049 " pdb=" CA THR B1049 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.95e+00 bond pdb=" N LYS D1052 " pdb=" CA LYS D1052 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.15e-02 7.56e+03 5.73e+00 bond pdb=" N LYS B1052 " pdb=" CA LYS B1052 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.15e-02 7.56e+03 5.63e+00 bond pdb=" N SER B1050 " pdb=" CA SER B1050 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.61e+00 ... (remaining 19877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 26042 2.67 - 5.33: 664 5.33 - 8.00: 136 8.00 - 10.66: 20 10.66 - 13.33: 2 Bond angle restraints: 26864 Sorted by residual: angle pdb=" C ARG A1130 " pdb=" N HIS A1131 " pdb=" CA HIS A1131 " ideal model delta sigma weight residual 121.54 131.98 -10.44 1.91e+00 2.74e-01 2.99e+01 angle pdb=" C ARG C1130 " pdb=" N HIS C1131 " pdb=" CA HIS C1131 " ideal model delta sigma weight residual 121.54 131.96 -10.42 1.91e+00 2.74e-01 2.98e+01 angle pdb=" C LYS A1051 " pdb=" N LYS A1052 " pdb=" CA LYS A1052 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" C LYS C1051 " pdb=" N LYS C1052 " pdb=" CA LYS C1052 " ideal model delta sigma weight residual 121.54 131.70 -10.16 1.91e+00 2.74e-01 2.83e+01 angle pdb=" C GLY D1161 " pdb=" N ASP D1162 " pdb=" CA ASP D1162 " ideal model delta sigma weight residual 123.10 128.13 -5.03 9.60e-01 1.09e+00 2.74e+01 ... (remaining 26859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 11389 24.69 - 49.38: 374 49.38 - 74.07: 20 74.07 - 98.76: 13 98.76 - 123.45: 6 Dihedral angle restraints: 11802 sinusoidal: 4670 harmonic: 7132 Sorted by residual: dihedral pdb=" CA PRO D1083 " pdb=" C PRO D1083 " pdb=" N GLU D1084 " pdb=" CA GLU D1084 " ideal model delta harmonic sigma weight residual 180.00 127.09 52.91 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA PRO B1083 " pdb=" C PRO B1083 " pdb=" N GLU B1084 " pdb=" CA GLU B1084 " ideal model delta harmonic sigma weight residual 180.00 127.11 52.89 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 175.81 -82.81 1 1.00e+01 1.00e-02 8.40e+01 ... (remaining 11799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2619 0.082 - 0.164: 324 0.164 - 0.246: 36 0.246 - 0.328: 13 0.328 - 0.410: 6 Chirality restraints: 2998 Sorted by residual: chirality pdb=" CG LEU C1002 " pdb=" CB LEU C1002 " pdb=" CD1 LEU C1002 " pdb=" CD2 LEU C1002 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CG LEU A1002 " pdb=" CB LEU A1002 " pdb=" CD1 LEU A1002 " pdb=" CD2 LEU A1002 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CG LEU A1114 " pdb=" CB LEU A1114 " pdb=" CD1 LEU A1114 " pdb=" CD2 LEU A1114 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 2995 not shown) Planarity restraints: 3314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 513 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C GLY B 513 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY B 513 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 514 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 513 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C GLY D 513 " 0.042 2.00e-02 2.50e+03 pdb=" O GLY D 513 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL D 514 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 421 " 0.032 2.00e-02 2.50e+03 1.70e-02 5.76e+00 pdb=" CG TYR A 421 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 421 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 421 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 421 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 421 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 421 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 421 " 0.023 2.00e-02 2.50e+03 ... (remaining 3311 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2019 2.75 - 3.29: 20355 3.29 - 3.83: 32550 3.83 - 4.36: 37672 4.36 - 4.90: 63551 Nonbonded interactions: 156147 Sorted by model distance: nonbonded pdb=" O PHE D1106 " pdb=" OG SER D1147 " model vdw 2.214 3.040 nonbonded pdb=" O PHE B1106 " pdb=" OG SER B1147 " model vdw 2.214 3.040 nonbonded pdb=" O PHE C1106 " pdb=" OG SER C1147 " model vdw 2.252 3.040 nonbonded pdb=" O PHE A1106 " pdb=" OG SER A1147 " model vdw 2.253 3.040 nonbonded pdb=" O PRO C1107 " pdb=" OG SER C1110 " model vdw 2.295 3.040 ... (remaining 156142 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 42.210 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 19894 Z= 0.299 Angle : 1.077 13.326 26888 Z= 0.588 Chirality : 0.060 0.410 2998 Planarity : 0.006 0.049 3314 Dihedral : 12.009 123.452 7218 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.49 % Allowed : 2.56 % Favored : 96.95 % Rotamer: Outliers : 0.86 % Allowed : 4.74 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 2460 helix: -0.43 (0.11), residues: 1318 sheet: -0.85 (0.37), residues: 150 loop : -1.65 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 767 HIS 0.015 0.003 HIS C1204 PHE 0.036 0.003 PHE D1126 TYR 0.032 0.003 TYR A 421 ARG 0.006 0.001 ARG C1098 Details of bonding type rmsd hydrogen bonds : bond 0.22957 ( 1109) hydrogen bonds : angle 6.89563 ( 3243) SS BOND : bond 0.00287 ( 12) SS BOND : angle 2.55891 ( 24) covalent geometry : bond 0.00656 (19882) covalent geometry : angle 1.07523 (26864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7244 (tt0) cc_final: 0.6741 (tp30) REVERT: A 463 MET cc_start: 0.3776 (ptm) cc_final: 0.3395 (ttm) REVERT: A 474 ILE cc_start: 0.7567 (tt) cc_final: 0.7141 (mp) REVERT: A 478 PRO cc_start: 0.5035 (Cg_endo) cc_final: 0.4807 (Cg_exo) REVERT: A 486 GLU cc_start: 0.8233 (tp30) cc_final: 0.8008 (pt0) REVERT: A 489 ILE cc_start: 0.8137 (pt) cc_final: 0.7766 (pt) REVERT: A 500 ILE cc_start: 0.5864 (mt) cc_final: 0.5191 (mt) REVERT: A 503 MET cc_start: 0.4273 (ttt) cc_final: 0.3854 (ttt) REVERT: A 514 VAL cc_start: 0.8355 (m) cc_final: 0.7906 (m) REVERT: A 527 MET cc_start: 0.7122 (mtt) cc_final: 0.6190 (mpp) REVERT: A 528 CYS cc_start: 0.8896 (m) cc_final: 0.8528 (m) REVERT: A 573 ILE cc_start: 0.8216 (tt) cc_final: 0.8000 (tt) REVERT: A 587 GLN cc_start: 0.6730 (tp40) cc_final: 0.5513 (pt0) REVERT: A 606 TRP cc_start: 0.7270 (m-10) cc_final: 0.6881 (m100) REVERT: A 609 THR cc_start: 0.9303 (m) cc_final: 0.8954 (p) REVERT: A 627 GLU cc_start: 0.3901 (mt-10) cc_final: 0.2863 (pm20) REVERT: A 705 GLU cc_start: 0.5683 (mm-30) cc_final: 0.5414 (mm-30) REVERT: A 721 MET cc_start: 0.5743 (pp-130) cc_final: 0.5223 (mtp) REVERT: A 742 LEU cc_start: 0.5575 (mm) cc_final: 0.5040 (tp) REVERT: A 811 LEU cc_start: 0.8558 (mm) cc_final: 0.8286 (mm) REVERT: A 815 CYS cc_start: 0.7988 (m) cc_final: 0.7638 (p) REVERT: A 1025 ILE cc_start: 0.7984 (mm) cc_final: 0.7713 (tp) REVERT: A 1030 ASP cc_start: 0.7116 (p0) cc_final: 0.6880 (t70) REVERT: A 1059 HIS cc_start: 0.7750 (p-80) cc_final: 0.6474 (p-80) REVERT: A 1169 LYS cc_start: 0.5537 (mtpt) cc_final: 0.5297 (mtmm) REVERT: A 1174 SER cc_start: 0.6190 (p) cc_final: 0.5838 (t) REVERT: A 1191 MET cc_start: 0.7974 (tpp) cc_final: 0.7393 (tpp) REVERT: A 1194 VAL cc_start: 0.7339 (t) cc_final: 0.6968 (t) REVERT: A 1195 LEU cc_start: 0.8346 (mm) cc_final: 0.7954 (mm) outliers start: 6 outliers final: 0 residues processed: 182 average time/residue: 0.1749 time to fit residues: 39.6471 Evaluate side-chains 105 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.495 Evaluate side-chains 193 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 411 ASN cc_start: 0.7330 (p0) cc_final: 0.6215 (m-40) REVERT: B 414 MET cc_start: 0.8174 (mpt) cc_final: 0.7787 (ptt) REVERT: B 442 LEU cc_start: 0.7839 (mt) cc_final: 0.7251 (mt) REVERT: B 463 MET cc_start: 0.2474 (mtm) cc_final: 0.2053 (mtm) REVERT: B 471 LYS cc_start: 0.6431 (tppp) cc_final: 0.5932 (mttp) REVERT: B 486 GLU cc_start: 0.6890 (tp30) cc_final: 0.6360 (pt0) REVERT: B 511 LYS cc_start: 0.7235 (mmpt) cc_final: 0.6862 (mttt) REVERT: B 519 ASP cc_start: 0.8364 (t70) cc_final: 0.8132 (t0) REVERT: B 527 MET cc_start: 0.8577 (ttp) cc_final: 0.8211 (mmt) REVERT: B 538 VAL cc_start: 0.9070 (t) cc_final: 0.8839 (m) REVERT: B 594 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7517 (ttp-170) REVERT: B 616 TYR cc_start: 0.8441 (t80) cc_final: 0.8161 (t80) REVERT: B 679 PRO cc_start: 0.5498 (Cg_endo) cc_final: 0.4771 (Cg_exo) REVERT: B 688 GLU cc_start: 0.8133 (tt0) cc_final: 0.7719 (tp30) REVERT: B 704 LEU cc_start: 0.7781 (pt) cc_final: 0.7471 (pt) REVERT: B 708 MET cc_start: 0.8289 (tpp) cc_final: 0.7712 (tpp) REVERT: B 710 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7239 (mp0) REVERT: B 713 GLU cc_start: 0.6542 (mt-10) cc_final: 0.5977 (pt0) REVERT: B 714 GLN cc_start: 0.8055 (mm110) cc_final: 0.7621 (mm-40) REVERT: B 720 THR cc_start: 0.5703 (p) cc_final: 0.4742 (p) REVERT: B 752 LYS cc_start: 0.8310 (ttmt) cc_final: 0.8069 (ptpp) REVERT: B 768 TYR cc_start: 0.6598 (m-80) cc_final: 0.6292 (m-10) REVERT: B 769 ASP cc_start: 0.6883 (m-30) cc_final: 0.6517 (t0) REVERT: B 1040 LYS cc_start: 0.4632 (tppt) cc_final: 0.3899 (tppt) REVERT: B 1069 GLU cc_start: 0.6533 (tp30) cc_final: 0.6294 (tp30) REVERT: B 1087 ASP cc_start: 0.5784 (t70) cc_final: 0.4925 (p0) REVERT: B 1116 MET cc_start: 0.8489 (mmt) cc_final: 0.8259 (mmp) REVERT: B 1127 TYR cc_start: 0.5607 (m-10) cc_final: 0.5175 (m-80) REVERT: B 1191 MET cc_start: 0.8608 (mtt) cc_final: 0.8203 (mmm) REVERT: B 1195 LEU cc_start: 0.8827 (mt) cc_final: 0.8620 (mt) outliers start: 3 outliers final: 1 residues processed: 192 average time/residue: 0.1660 time to fit residues: 40.1668 Evaluate side-chains 113 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.3980 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 126 optimal weight: 0.0070 chunk 100 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 overall best weight: 1.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 HIS C 619 ASN C1148 ASN C1204 HIS Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN B 726 ASN B 791 ASN B1053 ASN B1081 HIS B1171 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.080019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.061531 restraints weight = 25803.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.063374 restraints weight = 15817.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.064663 restraints weight = 11376.550| |-----------------------------------------------------------------------------| r_work (final): 0.3268 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.061306 restraints weight = 24815.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.063102 restraints weight = 16076.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.064360 restraints weight = 11741.771| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19894 Z= 0.152 Angle : 0.662 7.208 26888 Z= 0.351 Chirality : 0.042 0.196 2998 Planarity : 0.005 0.054 3314 Dihedral : 8.710 103.428 2790 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.41 % Favored : 96.34 % Rotamer: Outliers : 0.19 % Allowed : 4.60 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 2460 helix: 1.64 (0.13), residues: 1340 sheet: -0.81 (0.36), residues: 152 loop : -1.29 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C1063 HIS 0.008 0.002 HIS B1131 PHE 0.039 0.002 PHE B 658 TYR 0.019 0.002 TYR C 450 ARG 0.008 0.001 ARG B 715 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 1109) hydrogen bonds : angle 4.44367 ( 3243) SS BOND : bond 0.00297 ( 12) SS BOND : angle 2.02855 ( 24) covalent geometry : bond 0.00328 (19882) covalent geometry : angle 0.65927 (26864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 402 GLU cc_start: 0.7913 (tt0) cc_final: 0.7658 (pt0) REVERT: C 405 TYR cc_start: 0.8387 (m-80) cc_final: 0.7865 (m-80) REVERT: C 406 VAL cc_start: 0.8678 (t) cc_final: 0.8250 (t) REVERT: C 407 MET cc_start: 0.8177 (ttm) cc_final: 0.7857 (mmm) REVERT: C 450 TYR cc_start: 0.5455 (m-80) cc_final: 0.4074 (m-80) REVERT: C 467 LEU cc_start: 0.7723 (mt) cc_final: 0.7494 (mt) REVERT: C 474 ILE cc_start: 0.8741 (tt) cc_final: 0.8339 (mp) REVERT: C 517 PHE cc_start: 0.7947 (p90) cc_final: 0.7490 (p90) REVERT: C 585 MET cc_start: 0.9104 (mmt) cc_final: 0.8889 (mmt) REVERT: C 586 GLN cc_start: 0.7463 (tp40) cc_final: 0.7213 (tp40) REVERT: C 587 GLN cc_start: 0.6763 (tp40) cc_final: 0.5954 (pt0) REVERT: C 606 TRP cc_start: 0.8008 (m-10) cc_final: 0.7290 (m100) REVERT: C 619 ASN cc_start: 0.7546 (t0) cc_final: 0.7268 (t0) REVERT: C 708 MET cc_start: 0.6664 (tpt) cc_final: 0.6222 (tpt) REVERT: C 1036 ARG cc_start: 0.6025 (mmm160) cc_final: 0.5512 (mmm-85) REVERT: C 1057 MET cc_start: 0.7601 (mmm) cc_final: 0.7352 (mmm) REVERT: C 1068 LEU cc_start: 0.8572 (mt) cc_final: 0.8333 (mt) REVERT: C 1081 HIS cc_start: 0.5962 (m170) cc_final: 0.5619 (m-70) REVERT: C 1082 PHE cc_start: 0.6838 (m-80) cc_final: 0.6541 (t80) REVERT: C 1147 SER cc_start: 0.8976 (t) cc_final: 0.8626 (p) REVERT: C 1190 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8760 (mt-10) REVERT: C 1191 MET cc_start: 0.7801 (tpp) cc_final: 0.7303 (tpp) REVERT: C 1195 LEU cc_start: 0.8124 (mm) cc_final: 0.7372 (mm) REVERT: C 1301 GLU cc_start: 0.5634 (tp30) cc_final: 0.5355 (pm20) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.1606 time to fit residues: 35.1041 Evaluate side-chains 112 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.581 Evaluate side-chains 138 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 395 VAL cc_start: 0.6544 (t) cc_final: 0.6236 (p) REVERT: B 408 MET cc_start: 0.6225 (mtt) cc_final: 0.4029 (tmm) REVERT: B 414 MET cc_start: 0.7802 (mpp) cc_final: 0.7377 (ptm) REVERT: B 471 LYS cc_start: 0.6491 (tppp) cc_final: 0.6013 (mttp) REVERT: B 504 ILE cc_start: 0.7788 (pt) cc_final: 0.7300 (pt) REVERT: B 511 LYS cc_start: 0.7071 (mmpt) cc_final: 0.6654 (mttm) REVERT: B 519 ASP cc_start: 0.8468 (t70) cc_final: 0.8231 (t0) REVERT: B 594 ARG cc_start: 0.7871 (ttp-170) cc_final: 0.7485 (ttp-170) REVERT: B 688 GLU cc_start: 0.8099 (tt0) cc_final: 0.7701 (tp30) REVERT: B 708 MET cc_start: 0.7879 (tpp) cc_final: 0.7653 (tpp) REVERT: B 721 MET cc_start: 0.7660 (tmm) cc_final: 0.7149 (ptm) REVERT: B 1069 GLU cc_start: 0.6512 (tp30) cc_final: 0.6145 (tp30) REVERT: B 1116 MET cc_start: 0.8392 (mmt) cc_final: 0.8017 (mmp) REVERT: B 1127 TYR cc_start: 0.5998 (m-10) cc_final: 0.5778 (m-80) REVERT: B 1146 LEU cc_start: 0.8615 (tt) cc_final: 0.8373 (tp) REVERT: B 1187 ILE cc_start: 0.8716 (mt) cc_final: 0.8369 (mt) REVERT: B 1191 MET cc_start: 0.8584 (mtt) cc_final: 0.8264 (mmm) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.1509 time to fit residues: 27.5212 Evaluate side-chains 91 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 32 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 202 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 154 optimal weight: 0.0970 chunk 209 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 709 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS B1008 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.080248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.061534 restraints weight = 26780.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.063444 restraints weight = 16237.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.064777 restraints weight = 11501.752| |-----------------------------------------------------------------------------| r_work (final): 0.3263 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.079163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.061075 restraints weight = 25276.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.062997 restraints weight = 16295.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.064348 restraints weight = 11786.266| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 19894 Z= 0.173 Angle : 0.875 21.334 26888 Z= 0.439 Chirality : 0.051 0.390 2998 Planarity : 0.006 0.059 3314 Dihedral : 8.484 96.543 2790 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.04 % Favored : 94.63 % Rotamer: Outliers : 1.34 % Allowed : 3.74 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2460 helix: 0.57 (0.13), residues: 1332 sheet: -1.40 (0.42), residues: 124 loop : -1.67 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP C 606 HIS 0.007 0.001 HIS C1059 PHE 0.065 0.003 PHE A 796 TYR 0.083 0.004 TYR A 702 ARG 0.012 0.001 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.04808 ( 1109) hydrogen bonds : angle 4.65401 ( 3243) SS BOND : bond 0.00472 ( 12) SS BOND : angle 1.82783 ( 24) covalent geometry : bond 0.00377 (19882) covalent geometry : angle 0.87366 (26864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 406 VAL cc_start: 0.8605 (t) cc_final: 0.8306 (t) REVERT: C 407 MET cc_start: 0.8243 (ttm) cc_final: 0.7847 (mmm) REVERT: C 432 ILE cc_start: 0.9076 (pt) cc_final: 0.8873 (mt) REVERT: C 450 TYR cc_start: 0.5734 (m-80) cc_final: 0.4695 (m-80) REVERT: C 467 LEU cc_start: 0.7862 (mt) cc_final: 0.7609 (mt) REVERT: C 474 ILE cc_start: 0.8728 (tt) cc_final: 0.8307 (mp) REVERT: C 517 PHE cc_start: 0.7950 (p90) cc_final: 0.7554 (p90) REVERT: C 570 GLU cc_start: 0.6494 (tm-30) cc_final: 0.6203 (tm-30) REVERT: C 587 GLN cc_start: 0.6657 (tp40) cc_final: 0.5701 (pt0) REVERT: C 606 TRP cc_start: 0.7991 (m-10) cc_final: 0.7296 (m100) REVERT: C 670 MET cc_start: 0.8380 (mmt) cc_final: 0.7994 (mmm) REVERT: C 692 ARG cc_start: 0.8000 (ttt90) cc_final: 0.7552 (ptm160) REVERT: C 708 MET cc_start: 0.6022 (tpt) cc_final: 0.5812 (tpt) REVERT: C 715 ARG cc_start: 0.7117 (mmm160) cc_final: 0.6912 (mmm160) REVERT: C 1057 MET cc_start: 0.7791 (mmm) cc_final: 0.7563 (mmm) REVERT: C 1068 LEU cc_start: 0.8628 (mt) cc_final: 0.8420 (mt) REVERT: C 1113 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8607 (mt) REVERT: C 1190 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8858 (mm-30) REVERT: C 1191 MET cc_start: 0.7660 (tpp) cc_final: 0.7404 (tpp) REVERT: C 1301 GLU cc_start: 0.6169 (tp30) cc_final: 0.5780 (pm20) outliers start: 14 outliers final: 1 residues processed: 158 average time/residue: 0.1461 time to fit residues: 30.3701 Evaluate side-chains 110 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.549 Evaluate side-chains 123 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 395 VAL cc_start: 0.6476 (t) cc_final: 0.6173 (p) REVERT: B 408 MET cc_start: 0.6197 (mtt) cc_final: 0.3810 (tmm) REVERT: B 414 MET cc_start: 0.7722 (mpp) cc_final: 0.7352 (ptt) REVERT: B 504 ILE cc_start: 0.7661 (pt) cc_final: 0.7108 (pt) REVERT: B 511 LYS cc_start: 0.7095 (mmpt) cc_final: 0.6583 (mttm) REVERT: B 519 ASP cc_start: 0.8422 (t70) cc_final: 0.8125 (t0) REVERT: B 594 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7414 (ttp-170) REVERT: B 688 GLU cc_start: 0.8123 (tt0) cc_final: 0.7589 (tp30) REVERT: B 704 LEU cc_start: 0.7793 (pp) cc_final: 0.7577 (pp) REVERT: B 708 MET cc_start: 0.8007 (tpp) cc_final: 0.7701 (tpp) REVERT: B 1068 LEU cc_start: 0.7470 (pp) cc_final: 0.6818 (pp) REVERT: B 1069 GLU cc_start: 0.6466 (tp30) cc_final: 0.5913 (mp0) REVERT: B 1091 ASP cc_start: 0.6768 (t0) cc_final: 0.6420 (p0) REVERT: B 1127 TYR cc_start: 0.6075 (m-10) cc_final: 0.5873 (m-80) REVERT: B 1187 ILE cc_start: 0.8741 (mt) cc_final: 0.8417 (mt) REVERT: B 1191 MET cc_start: 0.8556 (mtt) cc_final: 0.8281 (mmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1420 time to fit residues: 23.2731 Evaluate side-chains 84 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 108 optimal weight: 0.0980 chunk 192 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 176 optimal weight: 30.0000 chunk 180 optimal weight: 2.9990 chunk 36 optimal weight: 0.0030 chunk 93 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 575 ASN C1204 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1008 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.080930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.061984 restraints weight = 26426.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.063824 restraints weight = 16553.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.065176 restraints weight = 11907.996| |-----------------------------------------------------------------------------| r_work (final): 0.3284 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.079546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.061792 restraints weight = 25227.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.063625 restraints weight = 16341.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.064961 restraints weight = 11866.144| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 19894 Z= 0.194 Angle : 0.911 22.722 26888 Z= 0.462 Chirality : 0.060 0.853 2998 Planarity : 0.007 0.056 3314 Dihedral : 8.290 94.103 2790 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.20 % Favored : 94.39 % Rotamer: Outliers : 0.77 % Allowed : 4.69 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2460 helix: 0.20 (0.13), residues: 1324 sheet: -1.77 (0.40), residues: 120 loop : -1.81 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 605 HIS 0.027 0.004 HIS C1204 PHE 0.079 0.004 PHE A 571 TYR 0.098 0.004 TYR A 616 ARG 0.041 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04923 ( 1109) hydrogen bonds : angle 4.64830 ( 3243) SS BOND : bond 0.00242 ( 12) SS BOND : angle 1.66677 ( 24) covalent geometry : bond 0.00450 (19882) covalent geometry : angle 0.91031 (26864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 406 VAL cc_start: 0.8710 (t) cc_final: 0.8329 (t) REVERT: C 407 MET cc_start: 0.8171 (ttm) cc_final: 0.7689 (mmm) REVERT: C 442 LEU cc_start: 0.8765 (mm) cc_final: 0.7920 (tp) REVERT: C 450 TYR cc_start: 0.5881 (m-80) cc_final: 0.4560 (m-80) REVERT: C 474 ILE cc_start: 0.8728 (tt) cc_final: 0.8310 (mp) REVERT: C 517 PHE cc_start: 0.7890 (p90) cc_final: 0.7629 (p90) REVERT: C 534 ILE cc_start: 0.8820 (mm) cc_final: 0.8619 (mm) REVERT: C 587 GLN cc_start: 0.6619 (tp40) cc_final: 0.5658 (pt0) REVERT: C 606 TRP cc_start: 0.7912 (m-10) cc_final: 0.7115 (m100) REVERT: C 644 GLU cc_start: 0.7322 (mp0) cc_final: 0.7082 (pm20) REVERT: C 670 MET cc_start: 0.8452 (mmt) cc_final: 0.8008 (mmp) REVERT: C 1025 ILE cc_start: 0.8303 (mm) cc_final: 0.8085 (pt) REVERT: C 1055 GLU cc_start: 0.1952 (OUTLIER) cc_final: 0.1674 (mm-30) REVERT: C 1068 LEU cc_start: 0.8594 (mt) cc_final: 0.8383 (mt) REVERT: C 1080 ASP cc_start: 0.7481 (m-30) cc_final: 0.7225 (t0) REVERT: C 1190 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8860 (mm-30) REVERT: C 1191 MET cc_start: 0.7646 (tpp) cc_final: 0.7351 (tpp) REVERT: C 1301 GLU cc_start: 0.6355 (tp30) cc_final: 0.5485 (pm20) outliers start: 8 outliers final: 2 residues processed: 140 average time/residue: 0.1416 time to fit residues: 26.4092 Evaluate side-chains 103 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.501 Evaluate side-chains 118 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 395 VAL cc_start: 0.6515 (t) cc_final: 0.6209 (p) REVERT: B 408 MET cc_start: 0.6236 (mtt) cc_final: 0.3878 (tmm) REVERT: B 414 MET cc_start: 0.7723 (mpp) cc_final: 0.7372 (ptt) REVERT: B 504 ILE cc_start: 0.7732 (pt) cc_final: 0.7326 (pt) REVERT: B 511 LYS cc_start: 0.7008 (mmpt) cc_final: 0.6449 (mttm) REVERT: B 519 ASP cc_start: 0.8388 (t70) cc_final: 0.8061 (t0) REVERT: B 594 ARG cc_start: 0.7692 (ttp-170) cc_final: 0.7390 (ttp-170) REVERT: B 688 GLU cc_start: 0.8111 (tt0) cc_final: 0.7515 (tp30) REVERT: B 708 MET cc_start: 0.8001 (tpp) cc_final: 0.7708 (tpp) REVERT: B 1023 MET cc_start: 0.8859 (mmm) cc_final: 0.8597 (mmm) REVERT: B 1068 LEU cc_start: 0.7493 (pp) cc_final: 0.6796 (pp) REVERT: B 1069 GLU cc_start: 0.6464 (tp30) cc_final: 0.5893 (mp0) REVERT: B 1091 ASP cc_start: 0.6657 (t0) cc_final: 0.6281 (p0) REVERT: B 1187 ILE cc_start: 0.8746 (mt) cc_final: 0.8424 (mt) REVERT: B 1191 MET cc_start: 0.8624 (mtt) cc_final: 0.8307 (mmm) REVERT: B 1202 ASP cc_start: 0.8661 (m-30) cc_final: 0.8424 (m-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1397 time to fit residues: 22.3088 Evaluate side-chains 87 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.2505 > 50: distance: 0 - 1: 34.198 distance: 1 - 2: 37.295 distance: 1 - 4: 17.942 distance: 2 - 3: 16.615 distance: 2 - 9: 39.374 distance: 4 - 5: 33.233 distance: 5 - 6: 8.314 distance: 6 - 7: 5.390 distance: 6 - 8: 12.702 distance: 9 - 10: 53.741 distance: 10 - 11: 42.649 distance: 11 - 12: 47.733 distance: 11 - 13: 40.446 distance: 13 - 14: 19.388 distance: 14 - 15: 37.935 distance: 14 - 17: 18.226 distance: 15 - 16: 24.470 distance: 15 - 19: 59.165 distance: 17 - 18: 34.803 distance: 19 - 20: 50.377 distance: 20 - 21: 45.599 distance: 20 - 23: 38.723 distance: 21 - 22: 60.708 distance: 21 - 27: 55.027 distance: 23 - 24: 14.242 distance: 24 - 25: 18.403 distance: 24 - 26: 16.567 distance: 27 - 28: 37.268 distance: 28 - 29: 32.936 distance: 28 - 31: 15.551 distance: 29 - 30: 42.332 distance: 29 - 35: 49.699 distance: 31 - 32: 29.950 distance: 31 - 33: 51.199 distance: 32 - 34: 26.036 distance: 35 - 36: 45.877 distance: 36 - 37: 49.355 distance: 36 - 39: 29.106 distance: 37 - 38: 58.925 distance: 37 - 41: 46.017 distance: 39 - 40: 21.872 distance: 41 - 42: 18.170 distance: 41 - 47: 40.246 distance: 42 - 43: 49.690 distance: 42 - 45: 39.027 distance: 43 - 44: 39.586 distance: 43 - 48: 20.572 distance: 45 - 46: 41.547 distance: 46 - 47: 35.000 distance: 48 - 49: 58.888 distance: 49 - 50: 11.013 distance: 49 - 52: 49.573 distance: 50 - 51: 48.995 distance: 50 - 59: 52.586 distance: 52 - 53: 39.696 distance: 53 - 54: 38.141 distance: 54 - 55: 31.320 distance: 55 - 56: 21.485 distance: 56 - 57: 41.316 distance: 56 - 58: 27.031 distance: 59 - 60: 31.390 distance: 60 - 61: 20.677 distance: 60 - 63: 34.039 distance: 61 - 62: 39.115 distance: 61 - 65: 50.135 distance: 63 - 64: 39.136 distance: 65 - 66: 5.709 distance: 66 - 67: 15.061 distance: 66 - 69: 27.842 distance: 67 - 68: 44.688 distance: 69 - 70: 10.547 distance: 70 - 71: 14.068 distance: 70 - 72: 23.369