Starting phenix.real_space_refine on Sun Jul 5 10:25:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8avc_15678/07_2026/8avc_15678.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avc_15678/07_2026/8avc_15678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8avc_15678/07_2026/8avc_15678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avc_15678/07_2026/8avc_15678.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8avc_15678/07_2026/8avc_15678.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8avc_15678/07_2026/8avc_15678.cif" model { file = "/net/cci-nas-00/data/ceres_data/8avc_15678/07_2026/8avc_15678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avc_15678/07_2026/8avc_15678.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11844 atoms to isotropic. 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 Ni 3 6.56 5 S 81 5.16 5 C 11199 2.51 5 N 2940 2.21 5 O 3282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17505 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "B" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4757 Classifications: {'peptide': 593} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555} Chain: "C" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "D" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4757 Classifications: {'peptide': 593} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555} Chain: "E" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "F" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4757 Classifications: {'peptide': 593} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.03, per 1000 atoms: 0.17 Number of scatterers: 17505 At special positions: 0 Unit cell: (137.614, 142.588, 169.116, 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) Ni 3 28.00 S 81 16.00 O 3282 8.00 N 2940 7.00 C 11199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 167 " distance=2.04 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 410 " distance=2.03 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 526 " distance=2.02 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 496 " distance=2.03 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 167 " distance=2.03 Simple disulfide: pdb=" SG CYS D 350 " - pdb=" SG CYS D 410 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 434 " - pdb=" SG CYS D 445 " distance=2.05 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS D 526 " distance=2.03 Simple disulfide: pdb=" SG CYS D 486 " - pdb=" SG CYS D 496 " distance=2.03 Simple disulfide: pdb=" SG CYS D 602 " - pdb=" SG CYS D 672 " distance=2.03 Simple disulfide: pdb=" SG CYS E 117 " - pdb=" SG CYS E 167 " distance=2.03 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 410 " distance=2.04 Simple disulfide: pdb=" SG CYS F 411 " - pdb=" SG CYS F 416 " distance=2.03 Simple disulfide: pdb=" SG CYS F 434 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 471 " - pdb=" SG CYS F 526 " distance=2.03 Simple disulfide: pdb=" SG CYS F 486 " - pdb=" SG CYS F 496 " distance=2.03 Simple disulfide: pdb=" SG CYS F 602 " - pdb=" SG CYS F 672 " 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: 1.29 Conformation dependent library (CDL) restraints added in 616.3 milliseconds 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4212 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 42 sheets defined 16.6% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 23 through 45 removed outlier: 3.823A pdb=" N ILE A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.655A pdb=" N GLN A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 71 through 89 removed outlier: 3.847A pdb=" N SER A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 116 Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.758A pdb=" N VAL A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 160 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.975A pdb=" N VAL B 533 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'C' and resid 23 through 45 removed outlier: 3.594A pdb=" N ILE C 45 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 50 removed outlier: 3.629A pdb=" N GLN C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 50' Processing helix chain 'C' and resid 71 through 89 removed outlier: 3.884A pdb=" N SER C 88 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 116 Processing helix chain 'C' and resid 130 through 138 removed outlier: 3.631A pdb=" N VAL C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 160 Processing helix chain 'D' and resid 528 through 533 removed outlier: 3.819A pdb=" N VAL D 533 " --> pdb=" O ASP D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 671 Processing helix chain 'D' and resid 732 through 736 Processing helix chain 'E' and resid 23 through 45 removed outlier: 3.527A pdb=" N ILE E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 50 removed outlier: 3.940A pdb=" N SER E 50 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 removed outlier: 3.793A pdb=" N SER E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 89 " --> pdb=" O VAL E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 116 Processing helix chain 'E' and resid 130 through 138 removed outlier: 3.801A pdb=" N VAL E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 160 Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 375 through 377 No H-bonds generated for 'chain 'F' and resid 375 through 377' Processing helix chain 'F' and resid 528 through 533 removed outlier: 3.868A pdb=" N VAL F 532 " --> pdb=" O LEU F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 736 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 246 removed outlier: 3.679A pdb=" N LEU B 240 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 242 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER B 255 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N MET B 244 " --> pdb=" O LYS B 253 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS B 253 " --> pdb=" O MET B 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 279 through 286 Processing sheet with id=AA4, first strand: chain 'B' and resid 332 through 334 Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 341 removed outlier: 3.571A pdb=" N GLU B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 341 removed outlier: 6.833A pdb=" N CYS B 410 " --> pdb=" O HIS B 417 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N HIS B 417 " --> pdb=" O CYS B 410 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N CYS B 416 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 433 through 436 Processing sheet with id=AA8, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.250A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.250A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 539 through 545 removed outlier: 3.672A pdb=" N VAL B 541 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N SER B 555 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA B 543 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS B 553 " --> pdb=" O ALA B 543 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 582 through 586 Processing sheet with id=AB3, first strand: chain 'B' and resid 643 through 648 Processing sheet with id=AB4, first strand: chain 'B' and resid 690 through 694 removed outlier: 5.842A pdb=" N TYR B 677 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 739 through 748 removed outlier: 5.459A pdb=" N LEU B 742 " --> pdb=" O THR B 757 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR B 757 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ALA B 744 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N SER B 755 " --> pdb=" O ALA B 744 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 753 " --> pdb=" O PRO B 746 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 782 through 787 removed outlier: 3.599A pdb=" N TYR B 767 " --> pdb=" O VAL B 812 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 240 through 246 removed outlier: 5.457A pdb=" N GLY D 241 " --> pdb=" O ASP D 257 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP D 257 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 279 through 286 Processing sheet with id=AB9, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AC1, first strand: chain 'D' and resid 337 through 340 removed outlier: 3.805A pdb=" N GLU D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 416 through 417 removed outlier: 7.468A pdb=" N CYS D 416 " --> pdb=" O THR E 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 433 through 436 Processing sheet with id=AC4, first strand: chain 'D' and resid 482 through 484 removed outlier: 4.177A pdb=" N LEU D 462 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 482 through 484 removed outlier: 4.177A pdb=" N LEU D 462 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 539 through 545 removed outlier: 4.102A pdb=" N VAL D 541 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER D 555 " --> pdb=" O VAL D 541 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA D 543 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS D 553 " --> pdb=" O ALA D 543 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 582 through 586 Processing sheet with id=AC8, first strand: chain 'D' and resid 643 through 648 Processing sheet with id=AC9, first strand: chain 'D' and resid 687 through 694 removed outlier: 5.788A pdb=" N TYR D 677 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 739 through 745 Processing sheet with id=AD2, first strand: chain 'D' and resid 782 through 787 removed outlier: 3.642A pdb=" N TYR D 767 " --> pdb=" O VAL D 812 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS D 773 " --> pdb=" O GLN D 806 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 240 through 246 removed outlier: 6.045A pdb=" N GLY F 241 " --> pdb=" O ASP F 257 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP F 257 " --> pdb=" O GLY F 241 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 279 through 286 Processing sheet with id=AD5, first strand: chain 'F' and resid 331 through 334 Processing sheet with id=AD6, first strand: chain 'F' and resid 337 through 341 Processing sheet with id=AD7, first strand: chain 'F' and resid 433 through 436 Processing sheet with id=AD8, first strand: chain 'F' and resid 482 through 484 removed outlier: 4.479A pdb=" N LEU F 462 " --> pdb=" O LYS F 484 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 482 through 484 removed outlier: 4.479A pdb=" N LEU F 462 " --> pdb=" O LYS F 484 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 539 through 545 removed outlier: 5.594A pdb=" N ASN F 540 " --> pdb=" O GLU F 557 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU F 557 " --> pdb=" O ASN F 540 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 582 through 586 Processing sheet with id=AE3, first strand: chain 'F' and resid 643 through 648 Processing sheet with id=AE4, first strand: chain 'F' and resid 687 through 694 removed outlier: 5.818A pdb=" N TYR F 677 " --> pdb=" O VAL F 693 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 739 through 745 Processing sheet with id=AE6, first strand: chain 'F' and resid 782 through 787 removed outlier: 3.544A pdb=" N TYR F 767 " --> pdb=" O VAL F 812 " (cutoff:3.500A) 790 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2938 1.32 - 1.46: 6297 1.46 - 1.59: 8585 1.59 - 1.73: 0 1.73 - 1.87: 114 Bond restraints: 17934 Sorted by residual: bond pdb=" CB GLN C 96 " pdb=" CG GLN C 96 " ideal model delta sigma weight residual 1.520 1.424 0.096 3.00e-02 1.11e+03 1.02e+01 bond pdb=" CD GLN C 96 " pdb=" NE2 GLN C 96 " ideal model delta sigma weight residual 1.328 1.274 0.054 2.10e-02 2.27e+03 6.67e+00 bond pdb=" CB ASN C 99 " pdb=" CG ASN C 99 " ideal model delta sigma weight residual 1.516 1.455 0.061 2.50e-02 1.60e+03 5.93e+00 bond pdb=" CG ASN A 103 " pdb=" OD1 ASN A 103 " ideal model delta sigma weight residual 1.231 1.186 0.045 1.90e-02 2.77e+03 5.51e+00 bond pdb=" CG GLN C 96 " pdb=" CD GLN C 96 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.44e+00 ... (remaining 17929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 24265 3.53 - 7.06: 147 7.06 - 10.59: 25 10.59 - 14.12: 2 14.12 - 17.65: 2 Bond angle restraints: 24441 Sorted by residual: angle pdb=" CB GLN C 96 " pdb=" CG GLN C 96 " pdb=" CD GLN C 96 " ideal model delta sigma weight residual 112.60 94.95 17.65 1.70e+00 3.46e-01 1.08e+02 angle pdb=" N CYS D 434 " pdb=" CA CYS D 434 " pdb=" C CYS D 434 " ideal model delta sigma weight residual 108.38 116.42 -8.04 1.35e+00 5.49e-01 3.55e+01 angle pdb=" N GLN C 96 " pdb=" CA GLN C 96 " pdb=" C GLN C 96 " ideal model delta sigma weight residual 111.36 104.87 6.49 1.09e+00 8.42e-01 3.55e+01 angle pdb=" C ASN A 103 " pdb=" CA ASN A 103 " pdb=" CB ASN A 103 " ideal model delta sigma weight residual 110.63 120.80 -10.17 1.85e+00 2.92e-01 3.02e+01 angle pdb=" CA ASN A 103 " pdb=" CB ASN A 103 " pdb=" CG ASN A 103 " ideal model delta sigma weight residual 112.60 118.09 -5.49 1.00e+00 1.00e+00 3.02e+01 ... (remaining 24436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 10063 17.59 - 35.19: 653 35.19 - 52.78: 101 52.78 - 70.38: 27 70.38 - 87.97: 10 Dihedral angle restraints: 10854 sinusoidal: 4368 harmonic: 6486 Sorted by residual: dihedral pdb=" CA ILE D 501 " pdb=" C ILE D 501 " pdb=" N PHE D 502 " pdb=" CA PHE D 502 " ideal model delta harmonic sigma weight residual 180.00 137.16 42.84 0 5.00e+00 4.00e-02 7.34e+01 dihedral pdb=" CB CYS B 350 " pdb=" SG CYS B 350 " pdb=" SG CYS B 410 " pdb=" CB CYS B 410 " ideal model delta sinusoidal sigma weight residual -86.00 -22.47 -63.53 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 496 " pdb=" CB CYS B 496 " ideal model delta sinusoidal sigma weight residual 93.00 30.11 62.89 1 1.00e+01 1.00e-02 5.23e+01 ... (remaining 10851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2636 0.106 - 0.211: 154 0.211 - 0.317: 8 0.317 - 0.422: 0 0.422 - 0.528: 1 Chirality restraints: 2799 Sorted by residual: chirality pdb=" CA ASN A 103 " pdb=" N ASN A 103 " pdb=" C ASN A 103 " pdb=" CB ASN A 103 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.97e+00 chirality pdb=" CB ILE E 69 " pdb=" CA ILE E 69 " pdb=" CG1 ILE E 69 " pdb=" CG2 ILE E 69 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CG LEU A 60 " pdb=" CB LEU A 60 " pdb=" CD1 LEU A 60 " pdb=" CD2 LEU A 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 2796 not shown) Planarity restraints: 3078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 96 " 0.022 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" CD GLN C 96 " -0.080 2.00e-02 2.50e+03 pdb=" OE1 GLN C 96 " 0.029 2.00e-02 2.50e+03 pdb=" NE2 GLN C 96 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 103 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" CG ASN A 103 " -0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN A 103 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 103 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 759 " -0.061 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO B 760 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 760 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 760 " -0.050 5.00e-02 4.00e+02 ... (remaining 3075 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 191 2.52 - 3.12: 13291 3.12 - 3.71: 28949 3.71 - 4.31: 39823 4.31 - 4.90: 63889 Nonbonded interactions: 146143 Sorted by model distance: nonbonded pdb=" OE1 GLN C 96 " pdb=" O ILE D 501 " model vdw 1.931 3.040 nonbonded pdb=" ND2 ASN A 103 " pdb=" N LEU B 504 " model vdw 1.987 3.200 nonbonded pdb=" NH1 ARG B 467 " pdb="NI NI B 901 " model vdw 2.014 2.260 nonbonded pdb=" NE2 GLN C 83 " pdb=" O ALA C 98 " model vdw 2.110 3.120 nonbonded pdb=" OH TYR B 409 " pdb=" CB SER C 141 " model vdw 2.122 3.440 ... (remaining 146138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.430 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 17955 Z= 0.169 Angle : 0.802 17.651 24483 Z= 0.445 Chirality : 0.052 0.528 2799 Planarity : 0.005 0.089 3078 Dihedral : 12.050 87.969 6579 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.31 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.18), residues: 2181 helix: -0.69 (0.26), residues: 327 sheet: 0.27 (0.17), residues: 847 loop : -0.08 (0.21), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 149 TYR 0.019 0.001 TYR D 268 PHE 0.052 0.001 PHE D 502 TRP 0.017 0.001 TRP B 447 HIS 0.006 0.001 HIS B 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (17934) covalent geometry : angle 0.79906 / 0.44 (24441) SS BOND : bond 0.00494 / 0.36 ( 21) SS BOND : angle 1.90445 / 1.21 ( 42) hydrogen bonds : bond 0.11941 / 8.68 ( 743) hydrogen bonds : angle 6.70910 / 4.74 ( 2076) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9694 (mt) cc_final: 0.9448 (mt) REVERT: A 102 GLU cc_start: 0.8540 (mp0) cc_final: 0.8269 (pm20) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0402 time to fit residues: 1.8230 Evaluate side-chains 32 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.037 Evaluate side-chains 35 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.5243 (ppp) cc_final: 0.4220 (pmm) REVERT: B 443 MET cc_start: 0.9131 (tpp) cc_final: 0.8734 (tpp) REVERT: B 548 ASN cc_start: 0.8571 (m-40) cc_final: 0.8304 (m-40) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0668 time to fit residues: 3.2553 Evaluate side-chains 31 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.0030 chunk 200 optimal weight: 0.0870 chunk 212 optimal weight: 9.9990 overall best weight: 1.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 363 GLN B 412 ASN B 489 GLN B 567 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.037885 restraints weight = 6774.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.039545 restraints weight = 4771.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.040901 restraints weight = 3599.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.042036 restraints weight = 2830.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.042956 restraints weight = 2299.690| |-----------------------------------------------------------------------------| r_work (final): 0.2912 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.075748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.059556 restraints weight = 29831.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.060065 restraints weight = 22057.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.059833 restraints weight = 9819.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.059740 restraints weight = 9663.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.060043 restraints weight = 8208.700| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 1.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17955 Z= 0.170 Angle : 0.680 7.395 24483 Z= 0.368 Chirality : 0.047 0.179 2799 Planarity : 0.005 0.051 3078 Dihedral : 5.582 59.447 2367 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.18), residues: 2181 helix: -0.09 (0.26), residues: 318 sheet: 0.18 (0.16), residues: 909 loop : 0.22 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 105 TYR 0.028 0.002 TYR E 140 PHE 0.010 0.001 PHE F 403 TRP 0.008 0.001 TRP D 447 HIS 0.005 0.001 HIS F 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (17934) covalent geometry : angle 0.67810 / 0.37 (24441) SS BOND : bond 0.00423 / 0.40 ( 21) SS BOND : angle 1.39216 / 1.23 ( 42) hydrogen bonds : bond 0.05090 / 3.48 ( 743) hydrogen bonds : angle 6.30246 / 4.39 ( 2076) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.028 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.9504 (m-30) cc_final: 0.9191 (p0) REVERT: A 139 LEU cc_start: 0.8978 (pt) cc_final: 0.8679 (mp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0553 time to fit residues: 2.3342 Evaluate side-chains 29 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.028 Evaluate side-chains 42 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.5118 (ppp) cc_final: 0.4388 (pmm) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0534 time to fit residues: 3.1248 Evaluate side-chains 31 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 203 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 148 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 140 optimal weight: 0.0040 overall best weight: 0.1928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN B 567 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 = 0.3140 r_free = 0.3140 target = 0.051956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.038883 restraints weight = 5960.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.040508 restraints weight = 4309.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.041846 restraints weight = 3315.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.042781 restraints weight = 2642.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.043783 restraints weight = 2206.052| |-----------------------------------------------------------------------------| r_work (final): 0.2920 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.077270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.060994 restraints weight = 29927.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.061674 restraints weight = 22452.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.061455 restraints weight = 10773.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.061570 restraints weight = 9130.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.062387 restraints weight = 7837.686| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 1.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17955 Z= 0.145 Angle : 0.689 11.179 24483 Z= 0.363 Chirality : 0.049 0.256 2799 Planarity : 0.005 0.053 3078 Dihedral : 5.402 52.712 2367 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2181 helix: 0.07 (0.29), residues: 303 sheet: 0.28 (0.16), residues: 909 loop : 0.13 (0.22), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 467 TYR 0.029 0.002 TYR A 140 PHE 0.022 0.002 PHE F 403 TRP 0.007 0.001 TRP F 662 HIS 0.005 0.001 HIS F 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (17934) covalent geometry : angle 0.68773 / 0.36 (24441) SS BOND : bond 0.00429 / 0.41 ( 21) SS BOND : angle 1.31556 / 1.15 ( 42) hydrogen bonds : bond 0.04530 / 3.14 ( 743) hydrogen bonds : angle 5.99099 / 4.17 ( 2076) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.3561 (p) cc_final: 0.3087 (p) REVERT: A 79 LEU cc_start: 0.9638 (mm) cc_final: 0.9419 (mm) REVERT: A 101 LEU cc_start: 0.9241 (mt) cc_final: 0.8990 (tt) REVERT: A 102 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8826 (mm-30) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0617 time to fit residues: 2.7787 Evaluate side-chains 26 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.047 Evaluate side-chains 41 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.5055 (ppp) cc_final: 0.4209 (pmm) REVERT: B 443 MET cc_start: 0.9475 (tpt) cc_final: 0.9181 (tpp) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0581 time to fit residues: 3.5196 Evaluate side-chains 30 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 137 optimal weight: 0.2980 chunk 134 optimal weight: 0.0170 chunk 171 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 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 = 0.3126 r_free = 0.3126 target = 0.051037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.038086 restraints weight = 6620.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.039488 restraints weight = 4966.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.040825 restraints weight = 3966.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.041831 restraints weight = 3255.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.042656 restraints weight = 2749.834| |-----------------------------------------------------------------------------| r_work (final): 0.2909 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.078496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.062381 restraints weight = 29845.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.062586 restraints weight = 21352.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.062605 restraints weight = 11567.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.063228 restraints weight = 8681.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.063152 restraints weight = 7938.612| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 1.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17955 Z= 0.129 Angle : 0.637 7.383 24483 Z= 0.337 Chirality : 0.046 0.191 2799 Planarity : 0.004 0.031 3078 Dihedral : 5.151 46.795 2367 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2181 helix: -0.30 (0.27), residues: 321 sheet: 0.32 (0.16), residues: 906 loop : 0.02 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 41 TYR 0.014 0.001 TYR C 140 PHE 0.006 0.001 PHE F 334 TRP 0.008 0.001 TRP B 447 HIS 0.004 0.001 HIS C 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (17934) covalent geometry : angle 0.63561 / 0.34 (24441) SS BOND : bond 0.00411 / 0.37 ( 21) SS BOND : angle 1.12488 / 0.91 ( 42) hydrogen bonds : bond 0.04151 / 2.86 ( 743) hydrogen bonds : angle 5.72926 / 4.02 ( 2076) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.9197 (mt) cc_final: 0.8965 (mt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0471 time to fit residues: 2.1053 Evaluate side-chains 28 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.044 Evaluate side-chains 39 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.4963 (ppp) cc_final: 0.4121 (pmm) REVERT: B 443 MET cc_start: 0.9404 (tpt) cc_final: 0.9015 (tpp) REVERT: B 617 LEU cc_start: 0.9390 (tt) cc_final: 0.9189 (mp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0767 time to fit residues: 4.0716 Evaluate side-chains 31 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 146 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 176 optimal weight: 0.6980 chunk 164 optimal weight: 7.9990 chunk 160 optimal weight: 0.0570 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 0.0570 chunk 13 optimal weight: 0.0040 chunk 4 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.3228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 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 = 0.3097 r_free = 0.3097 target = 0.050181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.037605 restraints weight = 6570.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.039208 restraints weight = 4702.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.040471 restraints weight = 3598.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.041497 restraints weight = 2881.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.042326 restraints weight = 2380.159| |-----------------------------------------------------------------------------| r_work (final): 0.2881 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.078519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.060035 restraints weight = 29817.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.060922 restraints weight = 14930.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.060957 restraints weight = 9024.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.060833 restraints weight = 7035.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.061098 restraints weight = 6972.463| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 1.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17955 Z= 0.122 Angle : 0.614 6.679 24483 Z= 0.326 Chirality : 0.045 0.167 2799 Planarity : 0.004 0.067 3078 Dihedral : 4.839 36.912 2367 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.18), residues: 2181 helix: -0.18 (0.28), residues: 324 sheet: 0.38 (0.16), residues: 921 loop : -0.01 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.014 0.001 TYR A 140 PHE 0.008 0.001 PHE B 334 TRP 0.007 0.001 TRP B 447 HIS 0.004 0.001 HIS F 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (17934) covalent geometry : angle 0.61258 / 0.33 (24441) SS BOND : bond 0.00384 / 0.37 ( 21) SS BOND : angle 1.03639 / 0.88 ( 42) hydrogen bonds : bond 0.03891 / 2.69 ( 743) hydrogen bonds : angle 5.42325 / 3.80 ( 2076) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ILE cc_start: 0.9221 (mm) cc_final: 0.8864 (mt) REVERT: A 58 THR cc_start: 0.3644 (p) cc_final: 0.3193 (p) REVERT: A 101 LEU cc_start: 0.9065 (mt) cc_final: 0.8852 (mt) REVERT: A 102 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8658 (mm-30) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0577 time to fit residues: 2.7537 Evaluate side-chains 29 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.046 Evaluate side-chains 40 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.4887 (ppp) cc_final: 0.4097 (pmm) REVERT: B 273 LEU cc_start: 0.9632 (pp) cc_final: 0.9385 (tt) REVERT: B 443 MET cc_start: 0.9401 (tpt) cc_final: 0.9188 (tpp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0630 time to fit residues: 3.5878 Evaluate side-chains 31 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 52 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 149 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 22 optimal weight: 0.0170 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 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 = 0.3134 r_free = 0.3134 target = 0.052156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.038238 restraints weight = 6878.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.039803 restraints weight = 5049.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.041186 restraints weight = 3988.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.042288 restraints weight = 3244.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.043064 restraints weight = 2718.067| |-----------------------------------------------------------------------------| r_work (final): 0.2903 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.077810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.061703 restraints weight = 29983.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.062841 restraints weight = 25560.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.062983 restraints weight = 10301.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.062971 restraints weight = 8598.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.063433 restraints weight = 7562.387| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 1.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17955 Z= 0.121 Angle : 0.617 7.678 24483 Z= 0.330 Chirality : 0.045 0.181 2799 Planarity : 0.004 0.055 3078 Dihedral : 4.690 29.614 2367 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 2181 helix: -0.22 (0.28), residues: 324 sheet: 0.47 (0.16), residues: 906 loop : -0.01 (0.22), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 41 TYR 0.012 0.001 TYR F 507 PHE 0.010 0.001 PHE F 334 TRP 0.007 0.001 TRP B 447 HIS 0.003 0.001 HIS F 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (17934) covalent geometry : angle 0.61670 / 0.33 (24441) SS BOND : bond 0.00380 / 0.36 ( 21) SS BOND : angle 0.91647 / 0.80 ( 42) hydrogen bonds : bond 0.03803 / 2.62 ( 743) hydrogen bonds : angle 5.40692 / 3.78 ( 2076) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9437 (pttp) cc_final: 0.9199 (pptt) REVERT: A 42 ILE cc_start: 0.9187 (mm) cc_final: 0.8834 (mt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0484 time to fit residues: 2.1912 Evaluate side-chains 31 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.045 Evaluate side-chains 35 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 ASP cc_start: 0.7993 (t0) cc_final: 0.7436 (p0) REVERT: B 261 MET cc_start: 0.4485 (ppp) cc_final: 0.3709 (pmm) REVERT: B 273 LEU cc_start: 0.9603 (pp) cc_final: 0.9339 (tt) REVERT: B 617 LEU cc_start: 0.9390 (tt) cc_final: 0.9142 (mp) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0663 time to fit residues: 3.2814 Evaluate side-chains 29 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 125 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 70 optimal weight: 0.0470 chunk 126 optimal weight: 0.0770 chunk 51 optimal weight: 0.1980 chunk 166 optimal weight: 0.0570 chunk 48 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 148 optimal weight: 0.8980 chunk 175 optimal weight: 0.0470 overall best weight: 0.0852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 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 = 0.3163 r_free = 0.3163 target = 0.052931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.039740 restraints weight = 6512.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.041472 restraints weight = 4718.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.042785 restraints weight = 3672.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.043604 restraints weight = 2986.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.044693 restraints weight = 2548.920| |-----------------------------------------------------------------------------| r_work (final): 0.2969 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.078663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.062666 restraints weight = 29700.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.063064 restraints weight = 23534.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.063771 restraints weight = 9912.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.063615 restraints weight = 7535.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.063931 restraints weight = 7215.753| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 1.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17955 Z= 0.125 Angle : 0.647 11.272 24483 Z= 0.344 Chirality : 0.047 0.303 2799 Planarity : 0.004 0.049 3078 Dihedral : 4.596 22.228 2367 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 2181 helix: -0.42 (0.28), residues: 324 sheet: 0.58 (0.17), residues: 912 loop : -0.06 (0.22), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 368 TYR 0.012 0.001 TYR B 507 PHE 0.010 0.001 PHE F 334 TRP 0.007 0.001 TRP B 447 HIS 0.003 0.001 HIS F 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (17934) covalent geometry : angle 0.64651 / 0.34 (24441) SS BOND : bond 0.00331 / 0.31 ( 21) SS BOND : angle 0.86324 / 0.76 ( 42) hydrogen bonds : bond 0.03723 / 2.56 ( 743) hydrogen bonds : angle 5.36284 / 3.77 ( 2076) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.044 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9421 (pttp) cc_final: 0.9185 (pptt) REVERT: A 42 ILE cc_start: 0.9088 (mm) cc_final: 0.8737 (mt) REVERT: A 89 LEU cc_start: 0.9141 (mm) cc_final: 0.8904 (tp) REVERT: A 101 LEU cc_start: 0.8804 (mt) cc_final: 0.8584 (mt) REVERT: A 102 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8405 (mm-30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0506 time to fit residues: 2.2548 Evaluate side-chains 29 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.034 Evaluate side-chains 34 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 ASP cc_start: 0.7854 (t0) cc_final: 0.7320 (p0) REVERT: B 261 MET cc_start: 0.4162 (ppp) cc_final: 0.3408 (pmm) REVERT: B 443 MET cc_start: 0.9341 (tpt) cc_final: 0.9087 (tpp) REVERT: B 545 ILE cc_start: 0.8603 (mp) cc_final: 0.8285 (tp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0615 time to fit residues: 2.9628 Evaluate side-chains 29 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 106 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 chunk 35 optimal weight: 0.0770 chunk 182 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 14 optimal weight: 0.0020 chunk 22 optimal weight: 0.2980 chunk 28 optimal weight: 8.9990 chunk 20 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 132 optimal weight: 0.3980 overall best weight: 0.2546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 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 = 0.3157 r_free = 0.3157 target = 0.052579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.040043 restraints weight = 6422.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.041698 restraints weight = 4493.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.042887 restraints weight = 3413.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.043999 restraints weight = 2764.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.044941 restraints weight = 2287.693| |-----------------------------------------------------------------------------| r_work (final): 0.2972 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.078567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.062380 restraints weight = 29423.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.063330 restraints weight = 24132.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.063952 restraints weight = 9802.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.063662 restraints weight = 8172.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.064246 restraints weight = 7318.723| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 1.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17955 Z= 0.120 Angle : 0.642 9.606 24483 Z= 0.340 Chirality : 0.046 0.289 2799 Planarity : 0.004 0.046 3078 Dihedral : 4.462 20.147 2367 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.18), residues: 2181 helix: -0.20 (0.29), residues: 303 sheet: 0.58 (0.17), residues: 906 loop : -0.02 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 656 TYR 0.008 0.001 TYR D 507 PHE 0.008 0.001 PHE B 334 TRP 0.011 0.001 TRP B 447 HIS 0.003 0.001 HIS B 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (17934) covalent geometry : angle 0.64157 / 0.34 (24441) SS BOND : bond 0.00355 / 0.34 ( 21) SS BOND : angle 0.94322 / 0.87 ( 42) hydrogen bonds : bond 0.03647 / 2.52 ( 743) hydrogen bonds : angle 5.26879 / 3.70 ( 2076) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9421 (pttp) cc_final: 0.9179 (pptt) REVERT: A 42 ILE cc_start: 0.9062 (mm) cc_final: 0.8714 (mt) REVERT: A 89 LEU cc_start: 0.9089 (mm) cc_final: 0.8867 (tp) REVERT: A 101 LEU cc_start: 0.8655 (mt) cc_final: 0.8412 (mt) REVERT: A 102 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8385 (mm-30) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0420 time to fit residues: 1.9679 Evaluate side-chains 34 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.043 Evaluate side-chains 34 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 ASP cc_start: 0.7579 (t0) cc_final: 0.7064 (p0) REVERT: B 261 MET cc_start: 0.4255 (ppp) cc_final: 0.3538 (pmm) REVERT: B 376 GLU cc_start: 0.9373 (mp0) cc_final: 0.9128 (mp0) REVERT: B 443 MET cc_start: 0.9527 (tpt) cc_final: 0.9102 (tpp) REVERT: B 545 ILE cc_start: 0.8562 (mp) cc_final: 0.8273 (tp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0642 time to fit residues: 3.1109 Evaluate side-chains 28 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 60 optimal weight: 0.0000 chunk 51 optimal weight: 0.0570 chunk 182 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 chunk 137 optimal weight: 0.0980 chunk 124 optimal weight: 0.0870 chunk 123 optimal weight: 2.9990 chunk 101 optimal weight: 0.0970 chunk 127 optimal weight: 0.0570 overall best weight: 0.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 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 = 0.3170 r_free = 0.3170 target = 0.053228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.039982 restraints weight = 6620.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.041645 restraints weight = 4739.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.043004 restraints weight = 3657.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.044015 restraints weight = 2958.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.044875 restraints weight = 2475.627| |-----------------------------------------------------------------------------| r_work (final): 0.2958 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.077863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.059518 restraints weight = 30506.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.060152 restraints weight = 15495.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.060538 restraints weight = 9014.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.060452 restraints weight = 7204.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.060841 restraints weight = 6945.904| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 1.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17955 Z= 0.121 Angle : 0.636 9.155 24483 Z= 0.336 Chirality : 0.046 0.275 2799 Planarity : 0.004 0.045 3078 Dihedral : 4.413 19.768 2367 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 2181 helix: -0.20 (0.29), residues: 303 sheet: 0.56 (0.16), residues: 930 loop : -0.02 (0.22), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 105 TYR 0.008 0.001 TYR D 507 PHE 0.009 0.001 PHE F 334 TRP 0.008 0.001 TRP B 447 HIS 0.003 0.001 HIS B 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (17934) covalent geometry : angle 0.63559 / 0.34 (24441) SS BOND : bond 0.00523 / 0.50 ( 21) SS BOND : angle 0.90621 / 0.82 ( 42) hydrogen bonds : bond 0.03672 / 2.53 ( 743) hydrogen bonds : angle 5.16996 / 3.63 ( 2076) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9412 (pttp) cc_final: 0.9184 (pptt) REVERT: A 42 ILE cc_start: 0.9033 (mm) cc_final: 0.8586 (mt) REVERT: A 105 ARG cc_start: 0.8919 (mtp85) cc_final: 0.8401 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0617 time to fit residues: 2.8595 Evaluate side-chains 34 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.046 Evaluate side-chains 34 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 ASP cc_start: 0.7823 (t0) cc_final: 0.7267 (p0) REVERT: B 261 MET cc_start: 0.4560 (ppp) cc_final: 0.3892 (pmm) REVERT: B 376 GLU cc_start: 0.9391 (mp0) cc_final: 0.9140 (mp0) REVERT: B 443 MET cc_start: 0.9484 (tpt) cc_final: 0.9059 (tpp) REVERT: B 545 ILE cc_start: 0.8601 (mp) cc_final: 0.8258 (tp) REVERT: B 632 MET cc_start: 0.9340 (mpp) cc_final: 0.9133 (mpp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0776 time to fit residues: 3.5303 Evaluate side-chains 27 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 202 optimal weight: 0.3980 chunk 162 optimal weight: 0.0770 chunk 155 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 218 optimal weight: 9.9990 chunk 14 optimal weight: 0.2980 chunk 200 optimal weight: 0.7980 chunk 168 optimal weight: 0.0060 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 0.3980 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 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 = 0.3205 r_free = 0.3205 target = 0.053449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.040769 restraints weight = 6262.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.042326 restraints weight = 4576.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.043538 restraints weight = 3570.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.044584 restraints weight = 2919.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045386 restraints weight = 2444.908| |-----------------------------------------------------------------------------| r_work (final): 0.2988 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.076023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.057251 restraints weight = 33256.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.057236 restraints weight = 18173.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.058286 restraints weight = 12493.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.058238 restraints weight = 8897.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.058548 restraints weight = 7567.103| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 1.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17955 Z= 0.121 Angle : 0.651 8.723 24483 Z= 0.339 Chirality : 0.046 0.268 2799 Planarity : 0.004 0.045 3078 Dihedral : 4.418 19.078 2367 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2181 helix: -0.47 (0.28), residues: 321 sheet: 0.57 (0.16), residues: 930 loop : -0.02 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 675 TYR 0.007 0.001 TYR D 507 PHE 0.009 0.001 PHE D 334 TRP 0.009 0.001 TRP B 447 HIS 0.003 0.001 HIS B 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (17934) covalent geometry : angle 0.64731 / 0.34 (24441) SS BOND : bond 0.00401 / 0.38 ( 21) SS BOND : angle 1.77194 / 1.35 ( 42) hydrogen bonds : bond 0.03555 / 2.41 ( 743) hydrogen bonds : angle 5.17046 / 3.63 ( 2076) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9430 (pttp) cc_final: 0.9189 (pptt) REVERT: A 42 ILE cc_start: 0.8913 (mm) cc_final: 0.8573 (mt) REVERT: A 101 LEU cc_start: 0.8456 (mt) cc_final: 0.8226 (mt) REVERT: A 102 GLU cc_start: 0.9012 (tp30) cc_final: 0.8544 (mm-30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0610 time to fit residues: 2.8271 Evaluate side-chains 33 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.055 Evaluate side-chains 31 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 ASP cc_start: 0.7807 (t0) cc_final: 0.7286 (p0) REVERT: B 261 MET cc_start: 0.4656 (ppp) cc_final: 0.4004 (pmm) REVERT: B 443 MET cc_start: 0.9492 (tpt) cc_final: 0.9042 (tpp) REVERT: B 545 ILE cc_start: 0.8499 (mp) cc_final: 0.8147 (tp) REVERT: B 628 TYR cc_start: 0.8830 (m-10) cc_final: 0.8625 (m-10) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0930 time to fit residues: 3.8664 Evaluate side-chains 27 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 191 optimal weight: 8.9990 chunk 210 optimal weight: 0.9980 chunk 164 optimal weight: 0.0000 chunk 163 optimal weight: 0.0870 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 190 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 152 optimal weight: 0.7980 chunk 131 optimal weight: 0.0670 overall best weight: 0.3100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 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 = 0.3187 r_free = 0.3187 target = 0.053111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.040099 restraints weight = 6430.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.041477 restraints weight = 4683.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.042905 restraints weight = 3695.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.043980 restraints weight = 2992.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.044797 restraints weight = 2501.576| |-----------------------------------------------------------------------------| r_work (final): 0.2959 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.076014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.059363 restraints weight = 33475.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.059717 restraints weight = 20386.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.059779 restraints weight = 11861.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.059806 restraints weight = 8957.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.060721 restraints weight = 8071.833| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 1.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17955 Z= 0.119 Angle : 0.634 8.767 24483 Z= 0.334 Chirality : 0.046 0.269 2799 Planarity : 0.005 0.064 3078 Dihedral : 4.351 19.335 2367 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.19), residues: 2181 helix: -0.44 (0.29), residues: 321 sheet: 0.61 (0.16), residues: 927 loop : 0.02 (0.23), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 675 TYR 0.009 0.001 TYR B 333 PHE 0.008 0.001 PHE F 334 TRP 0.009 0.001 TRP B 447 HIS 0.003 0.001 HIS B 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (17934) covalent geometry : angle 0.63055 / 0.33 (24441) SS BOND : bond 0.00387 / 0.37 ( 21) SS BOND : angle 1.60752 / 1.22 ( 42) hydrogen bonds : bond 0.03522 / 2.41 ( 743) hydrogen bonds : angle 5.18622 / 3.64 ( 2076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1788.82 seconds wall clock time: 32 minutes 16.80 seconds (1936.80 seconds total)