Starting phenix.real_space_refine on Thu Jul 2 20:36:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8k3p_36855/07_2026/8k3p_36855.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3p_36855/07_2026/8k3p_36855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k3p_36855/07_2026/8k3p_36855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3p_36855/07_2026/8k3p_36855.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k3p_36855/07_2026/8k3p_36855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3p_36855/07_2026/8k3p_36855.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8k3p_36855/07_2026/8k3p_36855.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8k3p_36855/07_2026/8k3p_36855.cif" } resolution = 3.64 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 57 5.16 5 C 6464 2.51 5 N 1605 2.21 5 O 1778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s 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: 9906 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 4856 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 18, 'TRANS': 641} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 532 Unresolved non-hydrogen angles: 656 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ASN:plan1': 8, 'PHE:plan': 10, 'ASP:plan': 5, 'GLN:plan1': 9, 'TYR:plan': 1, 'ARG:plan': 8, 'GLU:plan': 21, 'TRP:plan': 2, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 299 Chain: "B" Number of atoms: 4884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 4884 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 18, 'TRANS': 641} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 502 Unresolved non-hydrogen angles: 616 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'ASN:plan1': 7, 'PHE:plan': 10, 'ASP:plan': 5, 'GLN:plan1': 8, 'TYR:plan': 1, 'ARG:plan': 8, 'GLU:plan': 20, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 279 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'POV': 1, 'VDG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'POV': 1, 'VDG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 2.20, per 1000 atoms: 0.22 Number of scatterers: 9906 At special positions: 0 Unit cell: (79.5, 134.62, 104.94, 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) S 57 16.00 P 2 15.00 O 1778 8.00 N 1605 7.00 C 6464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 379.5 milliseconds 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 66.6% alpha, 13.6% 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 392 through 401 Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.796A pdb=" N LYS A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.902A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 458 through 479 removed outlier: 3.642A pdb=" N LEU A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 506 through 517 removed outlier: 4.306A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.943A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 636 through 643 removed outlier: 5.819A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 658 Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.636A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 713 through 716 Processing helix chain 'A' and resid 717 through 726 removed outlier: 4.106A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 773 removed outlier: 4.473A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 781 Processing helix chain 'A' and resid 784 through 807 Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.527A pdb=" N SER A 811 " --> pdb=" O PHE A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 Processing helix chain 'A' and resid 862 through 895 Processing helix chain 'A' and resid 909 through 933 Processing helix chain 'A' and resid 936 through 940 Processing helix chain 'A' and resid 941 through 955 Proline residue: A 950 - end of helix Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 1028 through 1060 removed outlier: 3.604A pdb=" N VAL A1043 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A1044 " --> pdb=" O ARG A1040 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1075 removed outlier: 3.583A pdb=" N THR A1075 " --> pdb=" O LYS A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1129 removed outlier: 4.263A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.796A pdb=" N LYS B 414 " --> pdb=" O PRO B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 414' Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.902A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 458 through 479 removed outlier: 3.642A pdb=" N LEU B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 506 through 517 removed outlier: 4.307A pdb=" N LEU B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 Processing helix chain 'B' and resid 588 through 594 removed outlier: 3.944A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 618 Processing helix chain 'B' and resid 619 through 621 No H-bonds generated for 'chain 'B' and resid 619 through 621' Processing helix chain 'B' and resid 636 through 643 removed outlier: 5.901A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 658 Processing helix chain 'B' and resid 660 through 669 removed outlier: 3.636A pdb=" N PHE B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 713 through 716 Processing helix chain 'B' and resid 717 through 726 removed outlier: 4.105A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 773 removed outlier: 4.473A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 781 Processing helix chain 'B' and resid 784 through 807 Processing helix chain 'B' and resid 807 through 828 removed outlier: 3.527A pdb=" N SER B 811 " --> pdb=" O PHE B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 856 Processing helix chain 'B' and resid 862 through 895 Processing helix chain 'B' and resid 909 through 933 Processing helix chain 'B' and resid 936 through 940 Processing helix chain 'B' and resid 941 through 955 Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 1028 through 1060 removed outlier: 3.605A pdb=" N VAL B1043 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B1044 " --> pdb=" O ARG B1040 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1075 removed outlier: 3.584A pdb=" N THR B1075 " --> pdb=" O LYS B1071 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1129 removed outlier: 4.263A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 386 through 390 Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 390 removed outlier: 7.413A pdb=" N ILE A 493 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N LEU A 568 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 495 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N CYS A 570 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 497 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS A 572 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 12.242A pdb=" N VAL A 624 " --> pdb=" O TYR A 736 " (cutoff:3.500A) removed outlier: 15.510A pdb=" N ARG A 738 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 16.222A pdb=" N GLY A 626 " --> pdb=" O ARG A 738 " (cutoff:3.500A) removed outlier: 12.829A pdb=" N SER A 740 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N CYS A 628 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N ALA A 742 " --> pdb=" O CYS A 628 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLU A 630 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR A 744 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG A 632 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.908A pdb=" N SER A 555 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 386 through 390 Processing sheet with id=AA6, first strand: chain 'B' and resid 386 through 390 removed outlier: 7.388A pdb=" N ILE B 493 " --> pdb=" O GLN B 566 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N LEU B 568 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 495 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS B 570 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE B 497 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS B 572 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL B 624 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 10.798A pdb=" N TYR B 736 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N GLY B 626 " --> pdb=" O TYR B 736 " (cutoff:3.500A) removed outlier: 11.164A pdb=" N ARG B 738 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N CYS B 628 " --> pdb=" O ARG B 738 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER B 740 " --> pdb=" O CYS B 628 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AA8, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.908A pdb=" N SER B 555 " --> pdb=" O THR B 547 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 1968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1518 1.28 - 1.41: 2742 1.41 - 1.54: 5779 1.54 - 1.68: 11 1.68 - 1.81: 84 Bond restraints: 10134 Sorted by residual: bond pdb=" C22 VDG A1302 " pdb=" O01 VDG A1302 " ideal model delta sigma weight residual 1.388 1.670 -0.282 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C22 VDG B1302 " pdb=" O01 VDG B1302 " ideal model delta sigma weight residual 1.388 1.669 -0.281 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C21 VDG A1302 " pdb=" C22 VDG A1302 " ideal model delta sigma weight residual 1.530 1.309 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C21 VDG B1302 " pdb=" C22 VDG B1302 " ideal model delta sigma weight residual 1.530 1.309 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C19 VDG A1302 " pdb=" O01 VDG A1302 " ideal model delta sigma weight residual 1.425 1.273 0.152 2.00e-02 2.50e+03 5.81e+01 ... (remaining 10129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 12708 1.80 - 3.61: 1006 3.61 - 5.41: 91 5.41 - 7.21: 17 7.21 - 9.01: 8 Bond angle restraints: 13830 Sorted by residual: angle pdb=" CA GLY A 636 " pdb=" C GLY A 636 " pdb=" O GLY A 636 " ideal model delta sigma weight residual 122.57 118.23 4.34 9.20e-01 1.18e+00 2.23e+01 angle pdb=" C LEU B 635 " pdb=" CA LEU B 635 " pdb=" CB LEU B 635 " ideal model delta sigma weight residual 116.54 111.53 5.01 1.15e+00 7.56e-01 1.90e+01 angle pdb=" CA ILE A 391 " pdb=" C ILE A 391 " pdb=" O ILE A 391 " ideal model delta sigma weight residual 121.97 118.21 3.76 9.80e-01 1.04e+00 1.47e+01 angle pdb=" CA ILE B 391 " pdb=" C ILE B 391 " pdb=" O ILE B 391 " ideal model delta sigma weight residual 121.97 118.22 3.75 9.80e-01 1.04e+00 1.47e+01 angle pdb=" N PRO B 425 " pdb=" CA PRO B 425 " pdb=" C PRO B 425 " ideal model delta sigma weight residual 112.47 119.79 -7.32 2.06e+00 2.36e-01 1.26e+01 ... (remaining 13825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.48: 5787 33.48 - 66.97: 126 66.97 - 100.45: 11 100.45 - 133.94: 2 133.94 - 167.42: 2 Dihedral angle restraints: 5928 sinusoidal: 2032 harmonic: 3896 Sorted by residual: dihedral pdb=" C27 POV A1301 " pdb=" C28 POV A1301 " pdb=" C29 POV A1301 " pdb="C210 POV A1301 " ideal model delta sinusoidal sigma weight residual 127.48 -65.10 -167.42 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C27 POV B1301 " pdb=" C28 POV B1301 " pdb=" C29 POV B1301 " pdb="C210 POV B1301 " ideal model delta sinusoidal sigma weight residual 127.48 -65.12 -167.40 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C29 POV B1301 " pdb="C210 POV B1301 " pdb="C211 POV B1301 " pdb="C212 POV B1301 " ideal model delta sinusoidal sigma weight residual 112.25 -121.65 -126.10 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 5925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1170 0.062 - 0.124: 334 0.124 - 0.186: 120 0.186 - 0.248: 10 0.248 - 0.310: 2 Chirality restraints: 1636 Sorted by residual: chirality pdb=" C21 VDG A1302 " pdb=" C20 VDG A1302 " pdb=" C22 VDG A1302 " pdb=" O03 VDG A1302 " both_signs ideal model delta sigma weight residual False 2.75 2.44 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C21 VDG B1302 " pdb=" C20 VDG B1302 " pdb=" C22 VDG B1302 " pdb=" O03 VDG B1302 " both_signs ideal model delta sigma weight residual False 2.75 2.44 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA LEU B 734 " pdb=" N LEU B 734 " pdb=" C LEU B 734 " pdb=" CB LEU B 734 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1633 not shown) Planarity restraints: 1708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 424 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C GLU B 424 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU B 424 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO B 425 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 424 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.91e+00 pdb=" C GLU A 424 " 0.054 2.00e-02 2.50e+03 pdb=" O GLU A 424 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO A 425 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B1301 " -0.020 2.00e-02 2.50e+03 2.00e-02 3.98e+00 pdb=" C29 POV B1301 " 0.020 2.00e-02 2.50e+03 pdb="C210 POV B1301 " 0.020 2.00e-02 2.50e+03 pdb="C211 POV B1301 " -0.020 2.00e-02 2.50e+03 ... (remaining 1705 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2884 2.81 - 3.34: 10352 3.34 - 3.86: 16284 3.86 - 4.38: 17578 4.38 - 4.90: 29859 Nonbonded interactions: 76957 Sorted by model distance: nonbonded pdb=" O ALA B1069 " pdb=" OG SER B1072 " model vdw 2.293 3.040 nonbonded pdb=" O ALA A1069 " pdb=" OG SER A1072 " model vdw 2.293 3.040 nonbonded pdb=" O SER A1072 " pdb=" OG1 THR A1075 " model vdw 2.302 3.040 nonbonded pdb=" O SER B1072 " pdb=" OG1 THR B1075 " model vdw 2.302 3.040 nonbonded pdb=" O VAL A 421 " pdb=" N ALA A 534 " model vdw 2.371 3.120 ... (remaining 76952 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 382 through 577 or (resid 578 and (name N or name CA or na \ me C or name O or name CB )) or resid 579 through 1302)) selection = (chain 'B' and (resid 382 through 489 or (resid 490 through 492 and (name N or n \ ame CA or name C or name O or name CB )) or resid 493 through 575 or (resid 576 \ through 578 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 9 or (resid 580 and (name N or name CA or name C or name O or name CB )) or resi \ d 581 through 605 or (resid 606 and (name N or name CA or name C or name O or na \ me CB )) or resid 607 through 634 or (resid 635 and (name N or name CA or name C \ or name O or name CB )) or (resid 636 through 641 and (name N or name CA or nam \ e C or name O or name CB )) or resid 642 through 652 or (resid 653 and (name N o \ r name CA or name C or name O or name CB )) or resid 654 through 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.600 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.010 0.282 10134 Z= 0.610 Angle : 0.975 9.013 13830 Z= 0.670 Chirality : 0.066 0.310 1636 Planarity : 0.004 0.032 1708 Dihedral : 15.297 167.421 3408 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.22 % Allowed : 2.68 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.23), residues: 1300 helix: 0.98 (0.19), residues: 754 sheet: -0.74 (0.39), residues: 168 loop : -0.93 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 508 TYR 0.033 0.002 TYR B1097 PHE 0.011 0.001 PHE A 885 TRP 0.018 0.001 TRP A1103 HIS 0.002 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.01006 / 0.61 (10134) covalent geometry : angle 0.97522 / 0.67 (13830) hydrogen bonds : bond 0.16239 / 11.09 ( 667) hydrogen bonds : angle 6.41579 / 4.59 ( 1968) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.253 Fit side-chains REVERT: A 535 MET cc_start: 0.7965 (ttp) cc_final: 0.7664 (ttp) REVERT: A 583 ARG cc_start: 0.8479 (ttt180) cc_final: 0.8246 (ttm-80) REVERT: B 606 MET cc_start: 0.8388 (mmt) cc_final: 0.8082 (mmp) outliers start: 30 outliers final: 4 residues processed: 210 average time/residue: 0.0695 time to fit residues: 22.3235 Evaluate side-chains 140 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 942 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 HIS A 472 ASN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN A 658 ASN A1051 ASN B 459 HIS B 472 ASN ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B1051 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.124090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098545 restraints weight = 19994.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101917 restraints weight = 9675.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.104000 restraints weight = 6059.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.105608 restraints weight = 4575.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106504 restraints weight = 3765.092| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10134 Z= 0.148 Angle : 0.552 6.647 13830 Z= 0.298 Chirality : 0.042 0.161 1636 Planarity : 0.003 0.030 1708 Dihedral : 12.154 145.275 1591 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.00 % Allowed : 9.54 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.24), residues: 1300 helix: 1.94 (0.19), residues: 776 sheet: -0.23 (0.40), residues: 156 loop : -1.04 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B1112 TYR 0.014 0.001 TYR B1097 PHE 0.019 0.002 PHE A1124 TRP 0.011 0.001 TRP B1103 HIS 0.003 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (10134) covalent geometry : angle 0.55172 / 0.30 (13830) hydrogen bonds : bond 0.05452 / 3.67 ( 667) hydrogen bonds : angle 4.66263 / 3.31 ( 1968) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 583 ARG cc_start: 0.8320 (ttt180) cc_final: 0.8101 (ttm-80) REVERT: A 1112 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7588 (mtm110) REVERT: B 535 MET cc_start: 0.7082 (ttp) cc_final: 0.6802 (ttp) REVERT: B 1112 ARG cc_start: 0.7980 (mtm110) cc_final: 0.7474 (mtm180) outliers start: 28 outliers final: 19 residues processed: 183 average time/residue: 0.0678 time to fit residues: 19.2170 Evaluate side-chains 157 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 81 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 116 optimal weight: 0.0020 chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.124383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.098976 restraints weight = 19842.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.102348 restraints weight = 9554.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.104584 restraints weight = 6017.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.106133 restraints weight = 4484.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.106836 restraints weight = 3707.873| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10134 Z= 0.113 Angle : 0.509 6.947 13830 Z= 0.267 Chirality : 0.040 0.151 1636 Planarity : 0.003 0.027 1708 Dihedral : 11.727 161.351 1591 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.79 % Allowed : 12.65 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.24), residues: 1300 helix: 2.34 (0.19), residues: 764 sheet: -0.00 (0.40), residues: 160 loop : -0.71 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 508 TYR 0.011 0.001 TYR B1067 PHE 0.027 0.001 PHE B 569 TRP 0.009 0.001 TRP B1103 HIS 0.005 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (10134) covalent geometry : angle 0.50922 / 0.27 (13830) hydrogen bonds : bond 0.04703 / 3.13 ( 667) hydrogen bonds : angle 4.28582 / 3.05 ( 1968) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.372 Fit side-chains REVERT: A 510 LEU cc_start: 0.9090 (mt) cc_final: 0.8784 (mt) REVERT: A 535 MET cc_start: 0.7859 (ttp) cc_final: 0.7538 (ttp) REVERT: A 583 ARG cc_start: 0.8156 (ttt180) cc_final: 0.7728 (ttm-80) REVERT: A 692 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8334 (tp40) REVERT: A 814 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7988 (tp) REVERT: A 832 ASN cc_start: 0.6649 (OUTLIER) cc_final: 0.6384 (m-40) REVERT: A 850 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.7843 (t80) REVERT: A 1070 MET cc_start: 0.8201 (tmm) cc_final: 0.7844 (tmm) REVERT: A 1112 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7688 (mtm110) REVERT: B 535 MET cc_start: 0.7705 (ttp) cc_final: 0.7483 (ttp) REVERT: B 653 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8454 (tp30) REVERT: B 1112 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7688 (mtm110) outliers start: 26 outliers final: 14 residues processed: 168 average time/residue: 0.0676 time to fit residues: 17.7893 Evaluate side-chains 156 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 74 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 35 optimal weight: 0.0570 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.119927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.093637 restraints weight = 20245.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096845 restraints weight = 9863.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.099035 restraints weight = 6304.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100450 restraints weight = 4738.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.101391 restraints weight = 3973.535| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10134 Z= 0.163 Angle : 0.523 7.116 13830 Z= 0.279 Chirality : 0.040 0.160 1636 Planarity : 0.003 0.031 1708 Dihedral : 11.703 172.734 1589 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.75 % Allowed : 13.83 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.23), residues: 1300 helix: 2.23 (0.19), residues: 776 sheet: -0.01 (0.40), residues: 160 loop : -0.81 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 444 TYR 0.014 0.001 TYR B 878 PHE 0.024 0.002 PHE B 569 TRP 0.021 0.001 TRP B 490 HIS 0.005 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (10134) covalent geometry : angle 0.52282 / 0.28 (13830) hydrogen bonds : bond 0.04856 / 3.26 ( 667) hydrogen bonds : angle 4.16101 / 2.96 ( 1968) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7953 (ttp) REVERT: A 583 ARG cc_start: 0.8091 (ttt180) cc_final: 0.7653 (ttm-80) REVERT: A 692 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8416 (tp40) REVERT: A 832 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6604 (m-40) REVERT: A 850 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8084 (t80) REVERT: A 1112 ARG cc_start: 0.8027 (mtm180) cc_final: 0.7731 (mtm110) REVERT: B 653 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8361 (tp30) outliers start: 35 outliers final: 26 residues processed: 155 average time/residue: 0.0697 time to fit residues: 17.0253 Evaluate side-chains 159 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.117602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.091426 restraints weight = 20416.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094549 restraints weight = 10129.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096621 restraints weight = 6513.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097937 restraints weight = 4964.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.098662 restraints weight = 4198.554| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10134 Z= 0.169 Angle : 0.533 7.577 13830 Z= 0.284 Chirality : 0.041 0.158 1636 Planarity : 0.003 0.030 1708 Dihedral : 10.173 158.434 1588 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.64 % Allowed : 15.54 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.23), residues: 1300 helix: 2.21 (0.19), residues: 776 sheet: -0.15 (0.41), residues: 156 loop : -0.78 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1112 TYR 0.011 0.001 TYR B1097 PHE 0.029 0.002 PHE B 569 TRP 0.019 0.001 TRP B 490 HIS 0.005 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (10134) covalent geometry : angle 0.53256 / 0.28 (13830) hydrogen bonds : bond 0.04946 / 3.34 ( 667) hydrogen bonds : angle 4.10673 / 2.92 ( 1968) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.403 Fit side-chains REVERT: A 535 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8046 (ttp) REVERT: A 692 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8467 (tp40) REVERT: A 832 ASN cc_start: 0.7085 (OUTLIER) cc_final: 0.6605 (m-40) REVERT: A 850 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8184 (t80) REVERT: A 1070 MET cc_start: 0.8439 (tmm) cc_final: 0.7893 (tmm) REVERT: A 1112 ARG cc_start: 0.8043 (mtm180) cc_final: 0.7748 (mtm110) REVERT: B 476 MET cc_start: 0.8791 (mmt) cc_final: 0.8355 (mmm) REVERT: B 526 ASP cc_start: 0.7973 (p0) cc_final: 0.7509 (p0) REVERT: B 653 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8415 (tp30) REVERT: B 661 ASP cc_start: 0.8545 (m-30) cc_final: 0.8238 (m-30) REVERT: B 832 ASN cc_start: 0.7106 (OUTLIER) cc_final: 0.6422 (m110) REVERT: B 1112 ARG cc_start: 0.8017 (mtm180) cc_final: 0.7761 (mtm110) outliers start: 34 outliers final: 23 residues processed: 159 average time/residue: 0.0704 time to fit residues: 17.8277 Evaluate side-chains 155 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 2.9990 chunk 86 optimal weight: 0.0670 chunk 120 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.119846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.093530 restraints weight = 20240.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.096759 restraints weight = 9959.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.098863 restraints weight = 6355.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.100233 restraints weight = 4833.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.101144 restraints weight = 4070.836| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10134 Z= 0.114 Angle : 0.477 8.814 13830 Z= 0.252 Chirality : 0.039 0.154 1636 Planarity : 0.003 0.028 1708 Dihedral : 9.211 97.762 1588 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.36 % Allowed : 17.15 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.23), residues: 1300 helix: 2.31 (0.19), residues: 776 sheet: -0.08 (0.40), residues: 162 loop : -0.67 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 444 TYR 0.020 0.001 TYR B1097 PHE 0.019 0.001 PHE B 569 TRP 0.012 0.001 TRP B 490 HIS 0.005 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10134) covalent geometry : angle 0.47723 / 0.25 (13830) hydrogen bonds : bond 0.04370 / 2.93 ( 667) hydrogen bonds : angle 3.99992 / 2.85 ( 1968) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7920 (mm-40) REVERT: A 535 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.8051 (ttp) REVERT: A 832 ASN cc_start: 0.7031 (OUTLIER) cc_final: 0.6565 (m-40) REVERT: A 850 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8180 (t80) REVERT: A 1089 LEU cc_start: 0.7259 (mm) cc_final: 0.6919 (mt) REVERT: A 1112 ARG cc_start: 0.8023 (mtm180) cc_final: 0.7712 (mtm110) REVERT: B 476 MET cc_start: 0.8730 (mmt) cc_final: 0.8330 (mmm) REVERT: B 653 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8379 (tp30) REVERT: B 661 ASP cc_start: 0.8485 (m-30) cc_final: 0.8189 (m-30) outliers start: 22 outliers final: 17 residues processed: 156 average time/residue: 0.0693 time to fit residues: 17.3848 Evaluate side-chains 152 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 119 optimal weight: 7.9990 chunk 72 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 6 optimal weight: 0.0370 chunk 52 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.119507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092924 restraints weight = 20465.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.096135 restraints weight = 10221.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098295 restraints weight = 6604.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099651 restraints weight = 5035.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100522 restraints weight = 4262.758| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10134 Z= 0.121 Angle : 0.490 8.965 13830 Z= 0.256 Chirality : 0.039 0.153 1636 Planarity : 0.003 0.030 1708 Dihedral : 8.725 67.308 1588 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.79 % Allowed : 17.36 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.23), residues: 1300 helix: 2.32 (0.19), residues: 776 sheet: -0.04 (0.40), residues: 162 loop : -0.58 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1112 TYR 0.010 0.001 TYR A 827 PHE 0.027 0.001 PHE B 569 TRP 0.009 0.001 TRP B 490 HIS 0.005 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (10134) covalent geometry : angle 0.48998 / 0.26 (13830) hydrogen bonds : bond 0.04309 / 2.88 ( 667) hydrogen bonds : angle 3.93793 / 2.80 ( 1968) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7879 (mm-40) REVERT: A 535 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8081 (ttp) REVERT: A 832 ASN cc_start: 0.7022 (OUTLIER) cc_final: 0.6381 (m-40) REVERT: A 850 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8219 (t80) REVERT: A 1112 ARG cc_start: 0.7996 (mtm180) cc_final: 0.7658 (mtm110) REVERT: B 427 GLN cc_start: 0.9106 (pm20) cc_final: 0.8810 (pm20) REVERT: B 476 MET cc_start: 0.8771 (mmt) cc_final: 0.8373 (mmm) REVERT: B 653 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8354 (tp30) REVERT: B 661 ASP cc_start: 0.8512 (m-30) cc_final: 0.8215 (m-30) REVERT: B 832 ASN cc_start: 0.7040 (OUTLIER) cc_final: 0.6370 (m110) outliers start: 26 outliers final: 19 residues processed: 157 average time/residue: 0.0650 time to fit residues: 16.4133 Evaluate side-chains 160 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 49 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 GLN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.096484 restraints weight = 20875.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.099577 restraints weight = 10243.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.101687 restraints weight = 6559.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.102998 restraints weight = 4947.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.103734 restraints weight = 4155.348| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10134 Z= 0.273 Angle : 0.646 8.292 13830 Z= 0.340 Chirality : 0.043 0.165 1636 Planarity : 0.004 0.031 1708 Dihedral : 8.922 61.906 1588 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.86 % Allowed : 17.58 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.23), residues: 1300 helix: 1.88 (0.18), residues: 776 sheet: -0.44 (0.39), residues: 162 loop : -0.77 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 738 TYR 0.018 0.002 TYR B1097 PHE 0.028 0.002 PHE B 569 TRP 0.016 0.002 TRP A 806 HIS 0.003 0.001 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.27 (10134) covalent geometry : angle 0.64634 / 0.34 (13830) hydrogen bonds : bond 0.05613 / 3.79 ( 667) hydrogen bonds : angle 4.32188 / 3.09 ( 1968) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 427 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8407 (pm20) REVERT: A 437 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8069 (mm-40) REVERT: A 440 TYR cc_start: 0.8248 (m-10) cc_final: 0.8020 (m-80) REVERT: A 526 ASP cc_start: 0.8117 (p0) cc_final: 0.7775 (p0) REVERT: A 832 ASN cc_start: 0.7243 (OUTLIER) cc_final: 0.6728 (m-40) REVERT: B 661 ASP cc_start: 0.8499 (m-30) cc_final: 0.8041 (m-30) REVERT: B 832 ASN cc_start: 0.7164 (OUTLIER) cc_final: 0.6487 (m110) REVERT: B 1089 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7610 (mp) outliers start: 36 outliers final: 24 residues processed: 153 average time/residue: 0.0673 time to fit residues: 16.5741 Evaluate side-chains 155 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 93 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 75 optimal weight: 0.0170 chunk 114 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.127732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102432 restraints weight = 20113.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.105725 restraints weight = 9626.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.107938 restraints weight = 6065.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.109368 restraints weight = 4531.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.110245 restraints weight = 3771.589| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10134 Z= 0.109 Angle : 0.514 9.589 13830 Z= 0.266 Chirality : 0.040 0.153 1636 Planarity : 0.003 0.033 1708 Dihedral : 8.479 63.010 1584 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.68 % Allowed : 18.01 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.24), residues: 1300 helix: 2.24 (0.19), residues: 776 sheet: -0.25 (0.40), residues: 162 loop : -0.62 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1112 TYR 0.012 0.001 TYR A 827 PHE 0.033 0.001 PHE B 569 TRP 0.011 0.001 TRP B1103 HIS 0.006 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.11 (10134) covalent geometry : angle 0.51389 / 0.27 (13830) hydrogen bonds : bond 0.04403 / 2.95 ( 667) hydrogen bonds : angle 4.00533 / 2.85 ( 1968) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8119 (mm-40) REVERT: A 470 MET cc_start: 0.8226 (mtm) cc_final: 0.7991 (mtm) REVERT: A 832 ASN cc_start: 0.7165 (OUTLIER) cc_final: 0.6425 (m-40) REVERT: A 850 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8197 (t80) REVERT: A 1112 ARG cc_start: 0.7871 (mtm180) cc_final: 0.7549 (mtm180) REVERT: B 427 GLN cc_start: 0.9043 (pm20) cc_final: 0.8756 (pm20) REVERT: B 437 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8086 (mm-40) REVERT: B 476 MET cc_start: 0.8608 (mmt) cc_final: 0.8260 (mmm) REVERT: B 507 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7675 (tm-30) REVERT: B 653 GLU cc_start: 0.8745 (tp30) cc_final: 0.8441 (tp30) REVERT: B 832 ASN cc_start: 0.7002 (OUTLIER) cc_final: 0.6253 (m110) REVERT: B 1089 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7612 (mp) outliers start: 25 outliers final: 17 residues processed: 159 average time/residue: 0.0622 time to fit residues: 16.1869 Evaluate side-chains 154 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.126479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.101136 restraints weight = 20163.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.104398 restraints weight = 9862.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106592 restraints weight = 6255.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.107967 restraints weight = 4695.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.108743 restraints weight = 3927.224| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10134 Z= 0.135 Angle : 0.533 9.118 13830 Z= 0.279 Chirality : 0.040 0.154 1636 Planarity : 0.003 0.032 1708 Dihedral : 8.180 60.108 1584 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.68 % Allowed : 18.22 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.24), residues: 1300 helix: 2.28 (0.19), residues: 776 sheet: -0.22 (0.41), residues: 162 loop : -0.58 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1112 TYR 0.010 0.001 TYR A 827 PHE 0.031 0.001 PHE B 569 TRP 0.010 0.001 TRP B 806 HIS 0.004 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (10134) covalent geometry : angle 0.53262 / 0.28 (13830) hydrogen bonds : bond 0.04422 / 2.97 ( 667) hydrogen bonds : angle 3.99721 / 2.85 ( 1968) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7972 (mm-40) REVERT: A 832 ASN cc_start: 0.7124 (OUTLIER) cc_final: 0.6615 (m-40) REVERT: A 850 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8267 (t80) REVERT: B 427 GLN cc_start: 0.9046 (pm20) cc_final: 0.8763 (pm20) REVERT: B 437 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8033 (mm-40) REVERT: B 653 GLU cc_start: 0.8781 (tp30) cc_final: 0.8426 (tp30) REVERT: B 832 ASN cc_start: 0.7024 (OUTLIER) cc_final: 0.6288 (m110) outliers start: 25 outliers final: 19 residues processed: 153 average time/residue: 0.0625 time to fit residues: 15.7550 Evaluate side-chains 155 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 35 optimal weight: 0.0970 chunk 111 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.129984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.103105 restraints weight = 20180.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.106559 restraints weight = 9871.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.108865 restraints weight = 6311.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.110096 restraints weight = 4752.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111173 restraints weight = 4043.940| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10134 Z= 0.107 Angle : 0.508 9.171 13830 Z= 0.265 Chirality : 0.039 0.151 1636 Planarity : 0.003 0.032 1708 Dihedral : 7.936 59.285 1584 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.68 % Allowed : 18.33 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.24), residues: 1300 helix: 2.36 (0.19), residues: 778 sheet: -0.11 (0.41), residues: 162 loop : -0.50 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1112 TYR 0.015 0.001 TYR B 519 PHE 0.028 0.001 PHE B 569 TRP 0.008 0.001 TRP B 490 HIS 0.004 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (10134) covalent geometry : angle 0.50781 / 0.26 (13830) hydrogen bonds : bond 0.04053 / 2.71 ( 667) hydrogen bonds : angle 3.91280 / 2.78 ( 1968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1496.78 seconds wall clock time: 26 minutes 37.52 seconds (1597.52 seconds total)