Starting phenix.real_space_refine on Wed Jan 15 13:11:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fq3_29376/01_2025/8fq3_29376.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fq3_29376/01_2025/8fq3_29376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fq3_29376/01_2025/8fq3_29376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fq3_29376/01_2025/8fq3_29376.map" model { file = "/net/cci-nas-00/data/ceres_data/8fq3_29376/01_2025/8fq3_29376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fq3_29376/01_2025/8fq3_29376.cif" } resolution = 3.17 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= 0.003 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 64 5.16 5 Cl 4 4.86 5 C 5332 2.51 5 N 1384 2.21 5 O 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8386 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 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} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.91, per 1000 atoms: 0.70 Number of scatterers: 8386 At special positions: 0 Unit cell: (122.031, 95.823, 82.719, 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 64 16.00 O 1602 8.00 N 1384 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " 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: 2.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 18 sheets defined 44.0% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.677A 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 436 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.558A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.840A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.547A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 705 through 715 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 411 through 415 removed outlier: 3.577A pdb=" N LEU C 415 " --> pdb=" O HIS C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 4.059A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR C 421 " --> pdb=" O ASN C 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 421' 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 489 removed outlier: 3.731A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.587A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 removed outlier: 3.526A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 757 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.669A 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 436 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.527A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.845A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.501A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 705 through 715 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.565A pdb=" N LEU A 415 " --> pdb=" O HIS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.081A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR A 421 " --> pdb=" O ASN A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 421' 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 489 removed outlier: 3.779A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.600A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 768 Processing sheet with id=AA1, first strand: chain 'B' and resid 395 through 399 removed outlier: 7.014A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.747A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.747A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 502 through 505 removed outlier: 4.144A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 504 " --> pdb=" O MET B 721 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.752A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.143A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 476 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP C 490 " --> pdb=" O THR C 736 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.143A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 476 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.222A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 395 through 399 removed outlier: 7.052A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.739A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.739A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 502 through 505 removed outlier: 4.136A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.763A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.148A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 490 " --> pdb=" O THR A 736 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.148A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.219A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 936 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: 2.44 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2630 1.35 - 1.48: 2041 1.48 - 1.60: 3723 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C5 CYZ D1302 " pdb=" C6 CYZ D1302 " ideal model delta sigma weight residual 1.553 1.330 0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 11313 2.03 - 4.07: 133 4.07 - 6.10: 39 6.10 - 8.13: 27 8.13 - 10.17: 8 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 111.92 -10.17 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 111.86 -10.11 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.61 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " ideal model delta sigma weight residual 101.75 111.57 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" O3 CYZ B1302 " pdb=" S2 CYZ B1302 " pdb=" O4 CYZ B1302 " ideal model delta sigma weight residual 118.35 109.22 9.13 3.00e+00 1.11e-01 9.26e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.85: 4702 22.85 - 45.69: 455 45.69 - 68.54: 62 68.54 - 91.39: 19 91.39 - 114.24: 10 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: 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 93.00 164.22 -71.22 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 162.93 -69.93 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" CB CYS D 718 " pdb=" SG CYS D 718 " pdb=" SG CYS D 773 " pdb=" CB CYS D 773 " ideal model delta sinusoidal sigma weight residual -86.00 -46.99 -39.01 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1196 0.088 - 0.175: 72 0.175 - 0.263: 0 0.263 - 0.350: 0 0.350 - 0.438: 16 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C8 CYZ D1302 " pdb=" C1 CYZ D1302 " pdb=" N1 CYZ D1302 " pdb=" N2 CYZ D1302 " both_signs ideal model delta sigma weight residual False 2.20 2.64 -0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" C8 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" N1 CYZ B1302 " pdb=" N2 CYZ B1302 " both_signs ideal model delta sigma weight residual False 2.20 2.64 -0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" C8 CYZ A1302 " pdb=" C1 CYZ A1302 " pdb=" N1 CYZ A1302 " pdb=" N2 CYZ A1302 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.43 2.00e-01 2.50e+01 4.53e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 767 " 0.014 2.00e-02 2.50e+03 1.11e-02 3.09e+00 pdb=" CG TRP A 767 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 767 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 767 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 767 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 767 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 767 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 767 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 767 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 767 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 767 " -0.013 2.00e-02 2.50e+03 1.05e-02 2.77e+00 pdb=" CG TRP C 767 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP C 767 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 767 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 767 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 767 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 767 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 767 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 767 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 767 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 625 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C THR D 625 " 0.026 2.00e-02 2.50e+03 pdb=" O THR D 625 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL D 626 " -0.008 2.00e-02 2.50e+03 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 422 2.73 - 3.27: 8012 3.27 - 3.81: 13977 3.81 - 4.36: 16661 4.36 - 4.90: 28393 Nonbonded interactions: 67465 Sorted by model distance: nonbonded pdb=" OG SER C 497 " pdb=" O2 CYZ C1302 " model vdw 2.185 3.040 nonbonded pdb=" OG SER A 497 " pdb=" O2 CYZ A1302 " model vdw 2.185 3.040 nonbonded pdb=" NH1 ARG B 715 " pdb=" O TRP B 767 " model vdw 2.248 3.120 nonbonded pdb=" NH1 ARG D 715 " pdb=" O TRP D 767 " model vdw 2.262 3.120 nonbonded pdb=" O VAL D 681 " pdb=" OH TYR D 700 " model vdw 2.270 3.040 ... (remaining 67460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } 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: 2.050 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.950 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 0.015 0.243 8538 Z= 0.943 Angle : 0.702 10.167 11520 Z= 0.297 Chirality : 0.061 0.438 1284 Planarity : 0.003 0.026 1422 Dihedral : 17.770 114.236 3288 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 23.15 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.26), residues: 1044 helix: 1.22 (0.25), residues: 426 sheet: -0.93 (0.35), residues: 186 loop : -1.18 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 767 HIS 0.001 0.000 HIS B 412 PHE 0.008 0.001 PHE C 491 TYR 0.010 0.001 TYR C 424 ARG 0.002 0.000 ARG C 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.059 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2460 time to fit residues: 39.1349 Evaluate side-chains 117 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.195150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.175096 restraints weight = 11579.804| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.03 r_work: 0.4030 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8538 Z= 0.229 Angle : 0.544 6.415 11520 Z= 0.269 Chirality : 0.043 0.176 1284 Planarity : 0.004 0.034 1422 Dihedral : 9.378 83.677 1266 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.80 % Allowed : 20.69 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1044 helix: 1.12 (0.25), residues: 430 sheet: -0.91 (0.35), residues: 186 loop : -1.20 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 767 HIS 0.002 0.001 HIS D 412 PHE 0.009 0.001 PHE D 659 TYR 0.019 0.002 TYR C 424 ARG 0.002 0.000 ARG C 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.874 Fit side-chains REVERT: C 505 LYS cc_start: 0.5890 (mmtt) cc_final: 0.5371 (pptt) REVERT: C 647 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7035 (p90) REVERT: C 705 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6670 (mm-30) REVERT: D 466 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: A 505 LYS cc_start: 0.6261 (mmtt) cc_final: 0.5552 (pptt) REVERT: A 647 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.6992 (p90) REVERT: A 705 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6581 (mm-30) outliers start: 34 outliers final: 21 residues processed: 144 average time/residue: 0.2183 time to fit residues: 42.2117 Evaluate side-chains 143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.191003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.170382 restraints weight = 11722.173| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.14 r_work: 0.3967 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8538 Z= 0.269 Angle : 0.571 6.295 11520 Z= 0.285 Chirality : 0.045 0.227 1284 Planarity : 0.004 0.036 1422 Dihedral : 7.849 66.091 1266 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.81 % Allowed : 21.25 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1044 helix: 0.81 (0.25), residues: 432 sheet: -1.07 (0.36), residues: 176 loop : -1.31 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 767 HIS 0.002 0.001 HIS D 412 PHE 0.010 0.002 PHE D 495 TYR 0.022 0.002 TYR A 424 ARG 0.004 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.993 Fit side-chains REVERT: C 505 LYS cc_start: 0.6159 (mmtt) cc_final: 0.5547 (pptt) REVERT: C 647 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7324 (p90) REVERT: C 673 TYR cc_start: 0.6392 (t80) cc_final: 0.6138 (t80) REVERT: C 705 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7147 (mm-30) REVERT: D 466 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7395 (tt0) REVERT: D 668 ASP cc_start: 0.6634 (t0) cc_final: 0.6352 (t0) REVERT: D 764 ASN cc_start: 0.8114 (m110) cc_final: 0.7877 (m110) REVERT: A 505 LYS cc_start: 0.6486 (mmtt) cc_final: 0.5729 (pptt) REVERT: A 647 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7442 (p90) REVERT: A 705 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7024 (mm-30) outliers start: 43 outliers final: 29 residues processed: 155 average time/residue: 0.2267 time to fit residues: 47.8038 Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 7.9990 chunk 29 optimal weight: 0.0030 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 32 optimal weight: 0.0040 chunk 13 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.197748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.177986 restraints weight = 11533.063| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 2.05 r_work: 0.4058 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8538 Z= 0.137 Angle : 0.454 6.264 11520 Z= 0.232 Chirality : 0.041 0.168 1284 Planarity : 0.003 0.036 1422 Dihedral : 6.277 52.983 1266 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.68 % Allowed : 23.15 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1044 helix: 1.28 (0.26), residues: 430 sheet: -0.76 (0.36), residues: 186 loop : -1.19 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.001 0.000 HIS D 412 PHE 0.007 0.001 PHE D 659 TYR 0.007 0.001 TYR C 424 ARG 0.003 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.992 Fit side-chains REVERT: C 505 LYS cc_start: 0.6073 (mmtt) cc_final: 0.5472 (pptt) REVERT: C 642 GLN cc_start: 0.7352 (tm-30) cc_final: 0.6106 (mp10) REVERT: C 647 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7224 (p90) REVERT: D 764 ASN cc_start: 0.8133 (m110) cc_final: 0.7893 (m110) REVERT: A 505 LYS cc_start: 0.6005 (mmtt) cc_final: 0.5456 (pptt) REVERT: A 637 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7174 (tp30) REVERT: A 647 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7148 (p90) outliers start: 24 outliers final: 15 residues processed: 154 average time/residue: 0.2265 time to fit residues: 46.7514 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 61 optimal weight: 0.0030 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 0.0470 chunk 16 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.6092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 642 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.197472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.178189 restraints weight = 11563.675| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.98 r_work: 0.4067 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3950 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8538 Z= 0.144 Angle : 0.449 6.263 11520 Z= 0.230 Chirality : 0.041 0.135 1284 Planarity : 0.003 0.033 1422 Dihedral : 5.670 49.052 1266 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.91 % Allowed : 24.38 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1044 helix: 1.38 (0.26), residues: 430 sheet: -0.61 (0.36), residues: 184 loop : -1.16 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 767 HIS 0.001 0.000 HIS D 412 PHE 0.006 0.001 PHE D 659 TYR 0.010 0.001 TYR C 424 ARG 0.002 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.959 Fit side-chains REVERT: B 414 MET cc_start: 0.4562 (ppp) cc_final: 0.4358 (ppp) REVERT: B 459 ILE cc_start: 0.7299 (mm) cc_final: 0.6960 (mt) REVERT: C 505 LYS cc_start: 0.6141 (mmtt) cc_final: 0.5577 (pptt) REVERT: C 642 GLN cc_start: 0.7373 (tm-30) cc_final: 0.6174 (mp10) REVERT: C 647 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7151 (p90) REVERT: D 466 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: D 764 ASN cc_start: 0.8141 (m110) cc_final: 0.7866 (m110) REVERT: A 505 LYS cc_start: 0.6198 (mmtt) cc_final: 0.5638 (pptt) REVERT: A 647 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7167 (p90) outliers start: 26 outliers final: 18 residues processed: 150 average time/residue: 0.2279 time to fit residues: 46.4365 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.195442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.175785 restraints weight = 11532.703| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.04 r_work: 0.4030 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8538 Z= 0.174 Angle : 0.470 6.234 11520 Z= 0.240 Chirality : 0.041 0.132 1284 Planarity : 0.003 0.034 1422 Dihedral : 5.830 50.926 1266 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.91 % Allowed : 23.15 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1044 helix: 1.32 (0.26), residues: 430 sheet: -0.67 (0.36), residues: 184 loop : -1.19 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 767 HIS 0.001 0.001 HIS D 412 PHE 0.006 0.001 PHE D 659 TYR 0.013 0.001 TYR C 424 ARG 0.003 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.995 Fit side-chains REVERT: B 459 ILE cc_start: 0.7286 (mm) cc_final: 0.6945 (mt) REVERT: B 678 GLU cc_start: 0.7409 (pm20) cc_final: 0.7167 (pm20) REVERT: C 505 LYS cc_start: 0.6282 (mmtt) cc_final: 0.5682 (pptt) REVERT: C 642 GLN cc_start: 0.7414 (tm-30) cc_final: 0.6170 (mp10) REVERT: C 647 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7202 (p90) REVERT: C 705 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6754 (mm-30) REVERT: D 407 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.6276 (mmm) REVERT: D 466 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: D 642 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: D 764 ASN cc_start: 0.8082 (m110) cc_final: 0.7785 (m110) REVERT: A 505 LYS cc_start: 0.6297 (mmtt) cc_final: 0.5657 (pptt) REVERT: A 647 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7250 (p90) REVERT: A 705 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6798 (mm-30) outliers start: 35 outliers final: 24 residues processed: 152 average time/residue: 0.2286 time to fit residues: 46.6144 Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 642 GLN Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.196597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.176992 restraints weight = 11666.198| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.04 r_work: 0.4036 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3915 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8538 Z= 0.161 Angle : 0.462 6.213 11520 Z= 0.236 Chirality : 0.041 0.131 1284 Planarity : 0.003 0.034 1422 Dihedral : 5.753 50.637 1266 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.69 % Allowed : 23.27 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1044 helix: 1.35 (0.26), residues: 430 sheet: -0.68 (0.36), residues: 184 loop : -1.18 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 767 HIS 0.001 0.000 HIS D 412 PHE 0.006 0.001 PHE D 659 TYR 0.012 0.001 TYR A 424 ARG 0.003 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.140 Fit side-chains REVERT: B 459 ILE cc_start: 0.7238 (mm) cc_final: 0.6897 (mt) REVERT: C 505 LYS cc_start: 0.6260 (mmtt) cc_final: 0.5645 (pptt) REVERT: C 642 GLN cc_start: 0.7390 (tm-30) cc_final: 0.6155 (mp10) REVERT: C 647 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7125 (p90) REVERT: C 705 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6727 (mm-30) REVERT: D 407 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.6248 (mmm) REVERT: D 466 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: D 764 ASN cc_start: 0.8087 (m110) cc_final: 0.7779 (m110) REVERT: A 505 LYS cc_start: 0.6345 (mmtt) cc_final: 0.5707 (pptt) REVERT: A 647 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7265 (p90) REVERT: A 705 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6781 (mm-30) outliers start: 33 outliers final: 24 residues processed: 152 average time/residue: 0.2266 time to fit residues: 46.4603 Evaluate side-chains 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.193703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.174054 restraints weight = 11677.261| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.04 r_work: 0.4010 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3889 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8538 Z= 0.200 Angle : 0.499 7.007 11520 Z= 0.255 Chirality : 0.042 0.129 1284 Planarity : 0.004 0.057 1422 Dihedral : 6.031 50.967 1266 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.91 % Allowed : 23.60 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1044 helix: 1.23 (0.26), residues: 430 sheet: -0.82 (0.36), residues: 186 loop : -1.24 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 767 HIS 0.002 0.001 HIS D 412 PHE 0.008 0.001 PHE D 495 TYR 0.015 0.001 TYR C 424 ARG 0.003 0.000 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.949 Fit side-chains REVERT: B 407 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.6437 (mmm) REVERT: B 459 ILE cc_start: 0.7305 (mm) cc_final: 0.6971 (mt) REVERT: C 505 LYS cc_start: 0.6242 (mmtt) cc_final: 0.5702 (pptt) REVERT: C 642 GLN cc_start: 0.7405 (tm-30) cc_final: 0.6168 (mp10) REVERT: C 647 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7300 (p90) REVERT: C 705 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6761 (mm-30) REVERT: D 407 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.6315 (mmm) REVERT: D 466 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7354 (tt0) REVERT: D 764 ASN cc_start: 0.8085 (m110) cc_final: 0.7825 (m110) REVERT: A 505 LYS cc_start: 0.6154 (mmtt) cc_final: 0.5677 (pptt) REVERT: A 647 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7315 (p90) REVERT: A 705 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6846 (mm-30) outliers start: 35 outliers final: 26 residues processed: 153 average time/residue: 0.2322 time to fit residues: 47.8685 Evaluate side-chains 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 12 optimal weight: 0.1980 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 0.0370 chunk 23 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.198972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.179765 restraints weight = 11785.756| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 1.99 r_work: 0.4071 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3951 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8538 Z= 0.136 Angle : 0.456 5.791 11520 Z= 0.236 Chirality : 0.040 0.132 1284 Planarity : 0.003 0.036 1422 Dihedral : 5.522 50.855 1266 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.24 % Allowed : 24.27 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.26), residues: 1044 helix: 1.43 (0.26), residues: 430 sheet: -0.70 (0.36), residues: 186 loop : -1.14 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 767 HIS 0.001 0.000 HIS D 412 PHE 0.008 0.001 PHE A 495 TYR 0.011 0.001 TYR A 732 ARG 0.003 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.062 Fit side-chains REVERT: B 459 ILE cc_start: 0.7251 (mm) cc_final: 0.6926 (mt) REVERT: C 505 LYS cc_start: 0.6093 (mmtt) cc_final: 0.5754 (pptt) REVERT: C 637 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7197 (tp30) REVERT: C 642 GLN cc_start: 0.7365 (tm-30) cc_final: 0.6178 (mp10) REVERT: C 647 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.7135 (p90) REVERT: D 407 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.6352 (mmm) REVERT: D 466 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7308 (tt0) REVERT: D 764 ASN cc_start: 0.8145 (m110) cc_final: 0.7886 (m110) REVERT: A 505 LYS cc_start: 0.6116 (mmtt) cc_final: 0.5617 (pptt) REVERT: A 637 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7201 (tp30) REVERT: A 647 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7214 (p90) outliers start: 29 outliers final: 21 residues processed: 146 average time/residue: 0.2361 time to fit residues: 46.0509 Evaluate side-chains 151 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.7702 > 50: distance: 58 - 64: 29.036 distance: 59 - 83: 22.315 distance: 64 - 65: 44.705 distance: 65 - 66: 39.547 distance: 66 - 67: 26.572 distance: 66 - 68: 19.504 distance: 67 - 87: 34.199 distance: 68 - 69: 42.542 distance: 69 - 70: 38.143 distance: 69 - 72: 34.627 distance: 70 - 71: 33.689 distance: 70 - 76: 28.662 distance: 71 - 96: 35.942 distance: 72 - 73: 14.069 distance: 73 - 74: 12.211 distance: 74 - 75: 11.634 distance: 76 - 77: 7.220 distance: 77 - 78: 30.674 distance: 77 - 80: 31.581 distance: 78 - 79: 23.438 distance: 78 - 83: 27.137 distance: 79 - 104: 29.960 distance: 80 - 81: 18.149 distance: 80 - 82: 12.947 distance: 83 - 84: 26.786 distance: 84 - 85: 36.709 distance: 85 - 86: 46.580 distance: 85 - 87: 45.714 distance: 86 - 111: 32.979 distance: 87 - 88: 16.552 distance: 88 - 89: 27.416 distance: 88 - 91: 13.875 distance: 89 - 90: 15.369 distance: 89 - 96: 11.431 distance: 91 - 92: 12.156 distance: 92 - 93: 11.408 distance: 93 - 94: 13.801 distance: 93 - 95: 7.137 distance: 96 - 97: 22.892 distance: 97 - 98: 6.675 distance: 97 - 100: 26.944 distance: 98 - 99: 21.848 distance: 98 - 104: 41.504 distance: 100 - 101: 39.720 distance: 101 - 102: 39.935 distance: 101 - 103: 11.772 distance: 104 - 105: 19.380 distance: 105 - 106: 44.334 distance: 105 - 108: 11.633 distance: 106 - 107: 12.957 distance: 106 - 111: 25.652 distance: 108 - 109: 8.880 distance: 108 - 110: 12.045 distance: 111 - 112: 15.650 distance: 112 - 113: 17.426 distance: 112 - 115: 43.951 distance: 113 - 114: 40.986 distance: 113 - 123: 5.969 distance: 115 - 116: 33.151 distance: 116 - 117: 4.080 distance: 116 - 118: 36.321 distance: 117 - 119: 5.867 distance: 118 - 120: 11.903 distance: 119 - 121: 7.325 distance: 120 - 121: 37.882 distance: 121 - 122: 24.647 distance: 123 - 124: 26.114 distance: 124 - 125: 24.161 distance: 125 - 126: 11.792 distance: 125 - 127: 36.826 distance: 127 - 128: 8.214 distance: 128 - 129: 10.458 distance: 128 - 131: 17.146 distance: 129 - 130: 11.749 distance: 131 - 132: 7.111 distance: 132 - 133: 13.604 distance: 133 - 134: 14.034 distance: 134 - 135: 11.667