Starting phenix.real_space_refine on Sat Aug 23 06:07:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3p_36855/08_2025/8k3p_36855.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3p_36855/08_2025/8k3p_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_36855/08_2025/8k3p_36855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3p_36855/08_2025/8k3p_36855.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k3p_36855/08_2025/8k3p_36855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3p_36855/08_2025/8k3p_36855.map" } 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-2.0-5787/lib/python3.9/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: 2.54, per 1000 atoms: 0.26 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: 1.02 Conformation dependent library (CDL) restraints added in 405.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.39 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: 1.73 Time building geometry restraints manager: 1.28 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: 5799 33.48 - 66.97: 126 66.97 - 100.45: 11 100.45 - 133.94: 2 133.94 - 167.42: 2 Dihedral angle restraints: 5940 sinusoidal: 2044 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 5937 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: 0.630 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.530 Find NCS groups from input model: 0.160 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 15.318 167.421 3420 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 aren 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 covalent geometry : bond 0.01006 (10134) covalent geometry : angle 0.97522 (13830) hydrogen bonds : bond 0.16239 ( 667) hydrogen bonds : angle 6.41579 ( 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 : 0.383 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: 0.0749 time to fit residues: 23.9483 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 : 0.232 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3720 r_free = 0.3720 target = 0.124167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.098643 restraints weight = 19909.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.101975 restraints weight = 9672.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104258 restraints weight = 6113.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.105768 restraints weight = 4551.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.106741 restraints weight = 3771.472| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1787 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= 0.150 Angle : 0.557 7.184 13830 Z= 0.300 Chirality : 0.042 0.161 1636 Planarity : 0.003 0.030 1708 Dihedral : 12.248 149.715 1603 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.11 % Allowed : 9.75 % Favored : 87.14 % 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 aren not related in a simple way. whole: 1.22 (0.24), residues: 1300 helix: 1.92 (0.19), residues: 776 sheet: -0.39 (0.40), residues: 160 loop : -1.03 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B1112 TYR 0.013 0.002 TYR B1097 PHE 0.021 0.002 PHE B1124 TRP 0.011 0.001 TRP B1103 HIS 0.004 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00314 (10134) covalent geometry : angle 0.55695 (13830) hydrogen bonds : bond 0.05354 ( 667) hydrogen bonds : angle 4.63082 ( 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 197 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 583 ARG cc_start: 0.8264 (ttt180) cc_final: 0.8042 (ttm-80) REVERT: A 867 LEU cc_start: 0.8968 (tp) cc_final: 0.8760 (tp) REVERT: A 1112 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7653 (mtm110) REVERT: B 535 MET cc_start: 0.7080 (ttp) cc_final: 0.6809 (ttp) REVERT: B 1112 ARG cc_start: 0.8018 (mtm110) cc_final: 0.7512 (mtm180) outliers start: 29 outliers final: 20 residues processed: 184 average time/residue: 0.0747 time to fit residues: 21.2679 Evaluate side-chains 157 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 A residue 1122 VAL 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: 6.9990 chunk 98 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3693 r_free = 0.3693 target = 0.122206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096284 restraints weight = 19956.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099605 restraints weight = 9747.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.101809 restraints weight = 6203.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103314 restraints weight = 4667.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104065 restraints weight = 3887.268| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10134 Z= 0.132 Angle : 0.514 7.118 13830 Z= 0.272 Chirality : 0.041 0.167 1636 Planarity : 0.003 0.029 1708 Dihedral : 12.025 173.791 1603 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.22 % Allowed : 12.97 % Favored : 83.82 % 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 aren not related in a simple way. whole: 1.77 (0.24), residues: 1300 helix: 2.33 (0.19), residues: 764 sheet: -0.01 (0.40), residues: 160 loop : -0.75 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 508 TYR 0.017 0.001 TYR B 519 PHE 0.029 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 covalent geometry : bond 0.00284 (10134) covalent geometry : angle 0.51429 (13830) hydrogen bonds : bond 0.04880 ( 667) hydrogen bonds : angle 4.28016 ( 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 176 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 510 LEU cc_start: 0.9110 (mt) cc_final: 0.8827 (mt) REVERT: A 535 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7591 (ttp) REVERT: A 583 ARG cc_start: 0.8155 (ttt180) cc_final: 0.7711 (ttm-80) REVERT: A 692 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8454 (tp40) REVERT: A 814 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8148 (tp) REVERT: A 832 ASN cc_start: 0.6750 (OUTLIER) cc_final: 0.6439 (m-40) REVERT: A 850 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8033 (t80) REVERT: A 1070 MET cc_start: 0.8276 (tmm) cc_final: 0.7881 (tmm) REVERT: A 1112 ARG cc_start: 0.7982 (mtm180) cc_final: 0.7703 (mtm110) REVERT: B 535 MET cc_start: 0.7770 (ttp) cc_final: 0.7556 (ttp) REVERT: B 653 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8444 (tp30) REVERT: B 832 ASN cc_start: 0.6861 (OUTLIER) cc_final: 0.6656 (m-40) REVERT: B 1112 ARG cc_start: 0.8053 (mtm110) cc_final: 0.7706 (mtm110) outliers start: 30 outliers final: 18 residues processed: 168 average time/residue: 0.0742 time to fit residues: 19.3417 Evaluate side-chains 160 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 946 ILE 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 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 946 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 74 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3633 r_free = 0.3633 target = 0.117959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.091744 restraints weight = 20439.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094860 restraints weight = 10209.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096860 restraints weight = 6566.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098307 restraints weight = 5002.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099056 restraints weight = 4195.164| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10134 Z= 0.191 Angle : 0.552 7.411 13830 Z= 0.294 Chirality : 0.041 0.162 1636 Planarity : 0.003 0.030 1708 Dihedral : 11.421 172.643 1600 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.75 % Allowed : 14.58 % Favored : 81.67 % 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 aren not related in a simple way. whole: 1.55 (0.23), residues: 1300 helix: 2.13 (0.19), residues: 776 sheet: -0.10 (0.40), residues: 156 loop : -0.87 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 508 TYR 0.015 0.001 TYR A 878 PHE 0.017 0.002 PHE B 813 TRP 0.019 0.001 TRP B 490 HIS 0.005 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00432 (10134) covalent geometry : angle 0.55190 (13830) hydrogen bonds : bond 0.05126 ( 667) hydrogen bonds : angle 4.22374 ( 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 171 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 535 MET cc_start: 0.7979 (ttp) cc_final: 0.7663 (ttp) REVERT: A 692 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8527 (tp40) REVERT: A 792 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8266 (p) REVERT: A 832 ASN cc_start: 0.7069 (OUTLIER) cc_final: 0.6682 (m-40) REVERT: A 850 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8092 (t80) REVERT: A 867 LEU cc_start: 0.8957 (tp) cc_final: 0.8721 (tp) REVERT: A 1070 MET cc_start: 0.8265 (tmm) cc_final: 0.7831 (tmm) REVERT: A 1112 ARG cc_start: 0.8053 (mtm180) cc_final: 0.7771 (mtm110) REVERT: B 526 ASP cc_start: 0.7919 (p0) cc_final: 0.7444 (p0) REVERT: B 653 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8385 (tp30) outliers start: 35 outliers final: 26 residues processed: 159 average time/residue: 0.0673 time to fit residues: 16.7832 Evaluate side-chains 157 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 571 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 792 THR 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 466 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 482 SER 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: 0.7980 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 16 optimal weight: 0.0030 chunk 23 optimal weight: 0.0980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3684 r_free = 0.3684 target = 0.121652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.095434 restraints weight = 20056.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.098722 restraints weight = 9844.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.100845 restraints weight = 6275.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.102191 restraints weight = 4769.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.103153 restraints weight = 4025.635| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10134 Z= 0.105 Angle : 0.474 8.111 13830 Z= 0.251 Chirality : 0.039 0.150 1636 Planarity : 0.003 0.030 1708 Dihedral : 10.050 127.104 1600 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.11 % Allowed : 15.76 % Favored : 81.14 % 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 aren not related in a simple way. whole: 1.82 (0.24), residues: 1300 helix: 2.33 (0.19), residues: 770 sheet: -0.02 (0.41), residues: 158 loop : -0.64 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1112 TYR 0.017 0.001 TYR B1097 PHE 0.022 0.001 PHE B 569 TRP 0.017 0.001 TRP B 490 HIS 0.005 0.001 HIS B 459 Details of bonding type rmsd covalent geometry : bond 0.00205 (10134) covalent geometry : angle 0.47357 (13830) hydrogen bonds : bond 0.04325 ( 667) hydrogen bonds : angle 4.04372 ( 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 170 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 535 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7858 (ttp) REVERT: A 571 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8794 (tt) REVERT: A 692 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8461 (tp40) REVERT: A 832 ASN cc_start: 0.6960 (OUTLIER) cc_final: 0.6512 (m-40) REVERT: A 850 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8172 (t80) REVERT: A 1089 LEU cc_start: 0.7330 (mm) cc_final: 0.7014 (mt) REVERT: A 1112 ARG cc_start: 0.8025 (mtm180) cc_final: 0.7726 (mtm110) REVERT: B 526 ASP cc_start: 0.7905 (p0) cc_final: 0.7436 (p0) REVERT: B 653 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8383 (tp30) outliers start: 29 outliers final: 17 residues processed: 160 average time/residue: 0.0660 time to fit residues: 16.7733 Evaluate side-chains 157 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 571 LEU 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 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 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 3.9990 chunk 86 optimal weight: 0.0060 chunk 120 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 0.0970 chunk 105 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3676 r_free = 0.3676 target = 0.120939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094775 restraints weight = 20055.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098046 restraints weight = 9854.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100233 restraints weight = 6252.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.101605 restraints weight = 4712.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.102511 restraints weight = 3966.847| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10134 Z= 0.111 Angle : 0.477 8.588 13830 Z= 0.250 Chirality : 0.039 0.153 1636 Planarity : 0.003 0.030 1708 Dihedral : 9.202 79.576 1600 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.47 % Allowed : 17.04 % 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 aren not related in a simple way. whole: 1.82 (0.23), residues: 1300 helix: 2.32 (0.19), residues: 778 sheet: -0.06 (0.41), residues: 158 loop : -0.67 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1112 TYR 0.011 0.001 TYR A 827 PHE 0.018 0.001 PHE B 569 TRP 0.018 0.001 TRP B 490 HIS 0.004 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00235 (10134) covalent geometry : angle 0.47732 (13830) hydrogen bonds : bond 0.04199 ( 667) hydrogen bonds : angle 3.91227 ( 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 162 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7870 (mm-40) REVERT: A 535 MET cc_start: 0.8178 (ttp) cc_final: 0.7913 (ttp) REVERT: A 692 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8757 (mt0) REVERT: A 832 ASN cc_start: 0.7007 (OUTLIER) cc_final: 0.6572 (m-40) REVERT: A 850 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8212 (t80) REVERT: A 1073 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7429 (mt) REVERT: A 1089 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6987 (mt) REVERT: A 1112 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7699 (mtm110) REVERT: B 526 ASP cc_start: 0.7835 (p0) cc_final: 0.7335 (p0) REVERT: B 653 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8374 (tp30) outliers start: 23 outliers final: 14 residues processed: 154 average time/residue: 0.0689 time to fit residues: 16.7875 Evaluate side-chains 152 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 495 VAL 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 1089 LEU 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 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE 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: 0.0170 chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 6 optimal weight: 0.0000 chunk 52 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 23 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3703 r_free = 0.3703 target = 0.122799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096799 restraints weight = 19720.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.100098 restraints weight = 9722.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102263 restraints weight = 6162.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.103697 restraints weight = 4655.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104612 restraints weight = 3897.438| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10134 Z= 0.098 Angle : 0.467 9.025 13830 Z= 0.244 Chirality : 0.039 0.148 1636 Planarity : 0.003 0.030 1708 Dihedral : 8.943 78.233 1600 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.79 % Allowed : 17.26 % Favored : 79.96 % 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 aren not related in a simple way. whole: 1.88 (0.24), residues: 1300 helix: 2.34 (0.19), residues: 780 sheet: 0.01 (0.41), residues: 158 loop : -0.60 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1112 TYR 0.017 0.001 TYR B1097 PHE 0.016 0.001 PHE B 569 TRP 0.013 0.001 TRP B 490 HIS 0.005 0.001 HIS B 459 Details of bonding type rmsd covalent geometry : bond 0.00191 (10134) covalent geometry : angle 0.46678 (13830) hydrogen bonds : bond 0.03846 ( 667) hydrogen bonds : angle 3.86257 ( 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 174 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8204 (ttp) cc_final: 0.7959 (ttp) REVERT: A 738 ARG cc_start: 0.8355 (ptm-80) cc_final: 0.8077 (ptm-80) REVERT: A 832 ASN cc_start: 0.6836 (OUTLIER) cc_final: 0.6236 (m-40) REVERT: A 850 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8239 (t80) REVERT: A 1073 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7260 (mt) REVERT: A 1089 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7097 (mt) REVERT: A 1112 ARG cc_start: 0.7980 (mtm180) cc_final: 0.7684 (mtm180) REVERT: B 427 GLN cc_start: 0.9060 (pm20) cc_final: 0.8763 (pm20) REVERT: B 526 ASP cc_start: 0.7837 (p0) cc_final: 0.7344 (p0) REVERT: B 653 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8339 (tp30) REVERT: B 738 ARG cc_start: 0.8268 (ptm-80) cc_final: 0.7982 (ptm-80) REVERT: B 1089 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7556 (mp) outliers start: 26 outliers final: 17 residues processed: 165 average time/residue: 0.0706 time to fit residues: 18.3182 Evaluate side-chains 158 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 541 THR Chi-restraints excluded: chain A residue 563 VAL 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 1089 LEU 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 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 1089 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 49 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 0.0040 overall best weight: 1.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3646 r_free = 0.3646 target = 0.118646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.092050 restraints weight = 20702.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.095257 restraints weight = 10364.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097389 restraints weight = 6708.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.098772 restraints weight = 5114.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099531 restraints weight = 4313.743| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10134 Z= 0.150 Angle : 0.507 8.732 13830 Z= 0.268 Chirality : 0.040 0.156 1636 Planarity : 0.003 0.031 1708 Dihedral : 8.713 69.265 1600 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.68 % Allowed : 17.68 % Favored : 79.64 % 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 aren not related in a simple way. whole: 1.90 (0.24), residues: 1300 helix: 2.35 (0.19), residues: 776 sheet: -0.12 (0.40), residues: 162 loop : -0.47 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 738 TYR 0.013 0.001 TYR B1097 PHE 0.026 0.002 PHE B 569 TRP 0.011 0.001 TRP B 490 HIS 0.003 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00338 (10134) covalent geometry : angle 0.50669 (13830) hydrogen bonds : bond 0.04492 ( 667) hydrogen bonds : angle 3.86722 ( 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 159 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7989 (mm-40) REVERT: A 440 TYR cc_start: 0.8204 (m-10) cc_final: 0.7983 (m-80) REVERT: A 535 MET cc_start: 0.8278 (ttp) cc_final: 0.8035 (ttp) REVERT: A 832 ASN cc_start: 0.7134 (OUTLIER) cc_final: 0.6532 (m-40) REVERT: A 850 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8254 (t80) REVERT: A 1073 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7327 (mt) REVERT: A 1112 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7736 (mtm180) REVERT: B 606 MET cc_start: 0.8249 (mmp) cc_final: 0.8019 (mmp) REVERT: B 653 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8551 (tp30) outliers start: 25 outliers final: 16 residues processed: 152 average time/residue: 0.0645 time to fit residues: 15.8493 Evaluate side-chains 149 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 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 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 75 optimal weight: 0.2980 chunk 114 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3682 r_free = 0.3682 target = 0.121255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095200 restraints weight = 19974.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098472 restraints weight = 9851.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.100631 restraints weight = 6264.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.102031 restraints weight = 4739.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102908 restraints weight = 3989.004| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10134 Z= 0.100 Angle : 0.473 9.296 13830 Z= 0.245 Chirality : 0.039 0.151 1636 Planarity : 0.003 0.032 1708 Dihedral : 8.504 68.103 1600 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.14 % Allowed : 18.54 % 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 aren not related in a simple way. whole: 2.00 (0.24), residues: 1300 helix: 2.41 (0.19), residues: 780 sheet: -0.07 (0.41), residues: 162 loop : -0.43 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1112 TYR 0.019 0.001 TYR A1097 PHE 0.027 0.001 PHE B 569 TRP 0.012 0.001 TRP B 490 HIS 0.004 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00202 (10134) covalent geometry : angle 0.47326 (13830) hydrogen bonds : bond 0.03978 ( 667) hydrogen bonds : angle 3.76839 ( 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 163 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7896 (mm-40) REVERT: A 535 MET cc_start: 0.8262 (ttp) cc_final: 0.8061 (ttp) REVERT: A 738 ARG cc_start: 0.8384 (ptm-80) cc_final: 0.8069 (ptm-80) REVERT: A 832 ASN cc_start: 0.7022 (OUTLIER) cc_final: 0.6389 (m-40) REVERT: A 850 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8246 (t80) REVERT: A 1073 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7295 (mt) REVERT: A 1112 ARG cc_start: 0.7994 (mtm180) cc_final: 0.7678 (mtm180) REVERT: B 427 GLN cc_start: 0.9080 (pm20) cc_final: 0.8778 (pm20) REVERT: B 606 MET cc_start: 0.8191 (mmp) cc_final: 0.7924 (mmp) REVERT: B 653 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8339 (tp30) REVERT: B 738 ARG cc_start: 0.8273 (ptm-80) cc_final: 0.7981 (ptm-80) outliers start: 20 outliers final: 15 residues processed: 158 average time/residue: 0.0711 time to fit residues: 17.2227 Evaluate side-chains 152 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 1091 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 541 THR 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 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 0.8980 chunk 23 optimal weight: 0.0570 chunk 76 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3777 r_free = 0.3777 target = 0.127272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.101799 restraints weight = 20114.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.105074 restraints weight = 9868.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107267 restraints weight = 6300.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.108681 restraints weight = 4746.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.109584 restraints weight = 3964.661| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3818 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= 0.144 Angle : 0.509 8.718 13830 Z= 0.267 Chirality : 0.040 0.152 1636 Planarity : 0.003 0.030 1708 Dihedral : 8.186 65.110 1596 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.47 % Allowed : 18.65 % Favored : 78.89 % 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 aren not related in a simple way. whole: 1.96 (0.24), residues: 1300 helix: 2.40 (0.19), residues: 778 sheet: -0.16 (0.40), residues: 162 loop : -0.45 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1112 TYR 0.019 0.001 TYR B1097 PHE 0.029 0.001 PHE B 569 TRP 0.011 0.001 TRP B 806 HIS 0.004 0.001 HIS B 459 Details of bonding type rmsd covalent geometry : bond 0.00321 (10134) covalent geometry : angle 0.50919 (13830) hydrogen bonds : bond 0.04271 ( 667) hydrogen bonds : angle 3.83544 ( 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 160 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7817 (mm-40) REVERT: A 507 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7592 (tm-30) REVERT: A 832 ASN cc_start: 0.7138 (OUTLIER) cc_final: 0.6479 (m-40) REVERT: A 850 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8309 (t80) REVERT: A 1073 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7229 (mt) REVERT: A 1112 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7733 (mtm180) REVERT: B 427 GLN cc_start: 0.8990 (pm20) cc_final: 0.8690 (pm20) REVERT: B 606 MET cc_start: 0.8270 (mmp) cc_final: 0.7937 (mmp) REVERT: B 653 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8337 (tp30) REVERT: B 738 ARG cc_start: 0.8313 (ptm-80) cc_final: 0.8019 (ptm-80) outliers start: 23 outliers final: 18 residues processed: 155 average time/residue: 0.0648 time to fit residues: 15.9538 Evaluate side-chains 157 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 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 1091 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 541 THR 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 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 97 optimal weight: 0.0980 chunk 35 optimal weight: 7.9990 chunk 111 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3807 r_free = 0.3807 target = 0.129630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.104461 restraints weight = 20136.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.107810 restraints weight = 9647.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.110054 restraints weight = 6069.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.111506 restraints weight = 4535.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.112425 restraints weight = 3760.513| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3960 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= 0.101 Angle : 0.477 8.859 13830 Z= 0.248 Chirality : 0.039 0.149 1636 Planarity : 0.003 0.029 1708 Dihedral : 8.007 66.015 1596 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.36 % Allowed : 18.54 % 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 aren not related in a simple way. whole: 2.04 (0.24), residues: 1300 helix: 2.45 (0.19), residues: 780 sheet: -0.15 (0.40), residues: 162 loop : -0.39 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1112 TYR 0.010 0.001 TYR A 827 PHE 0.028 0.001 PHE B 569 TRP 0.012 0.001 TRP B 490 HIS 0.004 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00206 (10134) covalent geometry : angle 0.47687 (13830) hydrogen bonds : bond 0.03921 ( 667) hydrogen bonds : angle 3.77324 ( 1968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1488.93 seconds wall clock time: 26 minutes 25.49 seconds (1585.49 seconds total)