Starting phenix.real_space_refine on Sat Nov 16 02:39:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/11_2024/8k3p_36855.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/11_2024/8k3p_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/11_2024/8k3p_36855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/11_2024/8k3p_36855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/11_2024/8k3p_36855.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/11_2024/8k3p_36855.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 10, 'GLU:plan': 21, 'ARG:plan': 8} 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: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 10, 'GLU:plan': 20, 'ARG:plan': 8} 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: 6.24, per 1000 atoms: 0.63 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: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.16 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: 3.49 Time building geometry restraints manager: 3.15 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 1129 or resid 1301 through 130 \ 2)) 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 1129 or resid 1 \ 301 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.730 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- 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= 0.600 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 : 9.47 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), 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 TRP 0.018 0.001 TRP A1103 HIS 0.002 0.001 HIS B 582 PHE 0.011 0.001 PHE A 885 TYR 0.033 0.002 TYR B1097 ARG 0.006 0.001 ARG B 508 *********************** 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 : 1.202 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: 0.1771 time to fit residues: 55.6745 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 : 1.102 ------------------------------------------------------------------------------- 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 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 119 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 B 459 HIS B 472 ASN ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10134 Z= 0.183 Angle : 0.548 6.731 13830 Z= 0.294 Chirality : 0.041 0.159 1636 Planarity : 0.003 0.030 1708 Dihedral : 12.188 146.513 1603 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.89 % Allowed : 10.18 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1300 helix: 2.05 (0.19), residues: 764 sheet: -0.37 (0.39), residues: 160 loop : -0.88 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1103 HIS 0.003 0.001 HIS B 459 PHE 0.021 0.002 PHE A1124 TYR 0.014 0.001 TYR B1097 ARG 0.003 0.001 ARG A 508 *********************** 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 191 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 583 ARG cc_start: 0.8293 (ttt180) cc_final: 0.8085 (ttm-80) REVERT: A 814 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8006 (tp) REVERT: A 832 ASN cc_start: 0.6742 (OUTLIER) cc_final: 0.6515 (m110) REVERT: A 1112 ARG cc_start: 0.7886 (mtm180) cc_final: 0.7403 (mtm180) REVERT: B 1112 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7470 (mtm180) outliers start: 27 outliers final: 16 residues processed: 181 average time/residue: 0.1735 time to fit residues: 47.8528 Evaluate side-chains 157 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 814 LEU Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN 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 B residue 469 ILE Chi-restraints excluded: chain B residue 513 LEU 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 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10134 Z= 0.194 Angle : 0.517 8.092 13830 Z= 0.275 Chirality : 0.041 0.156 1636 Planarity : 0.003 0.032 1708 Dihedral : 11.967 169.031 1602 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.22 % Allowed : 12.33 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1300 helix: 2.33 (0.19), residues: 764 sheet: 0.01 (0.40), residues: 160 loop : -0.73 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 490 HIS 0.005 0.001 HIS B 459 PHE 0.029 0.001 PHE B 569 TYR 0.013 0.001 TYR A1097 ARG 0.002 0.000 ARG B1112 *********************** 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 180 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 510 LEU cc_start: 0.9115 (mt) cc_final: 0.8873 (mt) REVERT: A 535 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7681 (ttp) REVERT: A 583 ARG cc_start: 0.8138 (ttt180) cc_final: 0.7712 (ttm-80) REVERT: A 692 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8358 (tp40) REVERT: A 850 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8057 (t80) REVERT: A 1070 MET cc_start: 0.8275 (tmm) cc_final: 0.7860 (tmm) REVERT: A 1112 ARG cc_start: 0.7980 (mtm180) cc_final: 0.7715 (mtm110) REVERT: B 653 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8397 (tp30) REVERT: B 832 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6720 (m-40) REVERT: B 1112 ARG cc_start: 0.8060 (mtm110) cc_final: 0.7701 (mtm110) outliers start: 30 outliers final: 17 residues processed: 167 average time/residue: 0.1655 time to fit residues: 42.3244 Evaluate side-chains 152 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 828 HIS Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.0970 chunk 120 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10134 Z= 0.153 Angle : 0.473 6.884 13830 Z= 0.254 Chirality : 0.039 0.152 1636 Planarity : 0.003 0.027 1708 Dihedral : 11.767 177.999 1600 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.89 % Allowed : 14.15 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.24), residues: 1300 helix: 2.34 (0.19), residues: 770 sheet: 0.07 (0.40), residues: 160 loop : -0.62 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 490 HIS 0.005 0.001 HIS A 459 PHE 0.017 0.001 PHE B 569 TYR 0.015 0.001 TYR B 440 ARG 0.003 0.000 ARG A 508 *********************** 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 174 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 535 MET cc_start: 0.8043 (ttp) cc_final: 0.7655 (ttp) REVERT: A 583 ARG cc_start: 0.8121 (ttt180) cc_final: 0.7717 (ttm-80) REVERT: A 692 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8342 (tp40) REVERT: A 832 ASN cc_start: 0.6900 (OUTLIER) cc_final: 0.6530 (m-40) REVERT: A 850 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8107 (t80) REVERT: A 875 MET cc_start: 0.8813 (mtp) cc_final: 0.8411 (mtm) REVERT: A 1112 ARG cc_start: 0.7991 (mtm180) cc_final: 0.7707 (mtm110) REVERT: B 454 MET cc_start: 0.7568 (mtp) cc_final: 0.7296 (mtm) REVERT: B 653 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8375 (tp30) REVERT: B 832 ASN cc_start: 0.6999 (OUTLIER) cc_final: 0.6664 (m110) REVERT: B 1112 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7687 (mtm110) outliers start: 27 outliers final: 20 residues processed: 162 average time/residue: 0.1721 time to fit residues: 43.2361 Evaluate side-chains 161 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 495 VAL Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 811 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 773 CYS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.1980 chunk 1 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10134 Z= 0.198 Angle : 0.487 7.168 13830 Z= 0.260 Chirality : 0.040 0.154 1636 Planarity : 0.003 0.028 1708 Dihedral : 10.471 146.853 1600 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.11 % Allowed : 15.11 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.23), residues: 1300 helix: 2.29 (0.19), residues: 776 sheet: 0.07 (0.40), residues: 160 loop : -0.70 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 490 HIS 0.004 0.001 HIS B 459 PHE 0.021 0.001 PHE A 569 TYR 0.010 0.001 TYR A 827 ARG 0.003 0.000 ARG B 444 *********************** 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 164 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: A 583 ARG cc_start: 0.8097 (ttt180) cc_final: 0.7692 (ttm-80) REVERT: A 692 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8400 (tp40) REVERT: A 832 ASN cc_start: 0.6979 (OUTLIER) cc_final: 0.6594 (m-40) REVERT: A 850 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8182 (t80) REVERT: A 1070 MET cc_start: 0.8411 (tmm) cc_final: 0.8052 (tmm) REVERT: A 1112 ARG cc_start: 0.8008 (mtm180) cc_final: 0.7705 (mtm110) REVERT: B 526 ASP cc_start: 0.7991 (p0) cc_final: 0.7491 (p0) REVERT: B 653 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8389 (tp30) REVERT: B 832 ASN cc_start: 0.7096 (OUTLIER) cc_final: 0.6826 (m-40) REVERT: B 1112 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7750 (mtm110) outliers start: 29 outliers final: 19 residues processed: 156 average time/residue: 0.1665 time to fit residues: 40.5227 Evaluate side-chains 151 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 773 CYS Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 106 optimal weight: 0.0970 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 30.0000 chunk 123 optimal weight: 1.9990 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10134 Z= 0.173 Angle : 0.471 7.970 13830 Z= 0.250 Chirality : 0.039 0.154 1636 Planarity : 0.003 0.027 1708 Dihedral : 9.356 79.998 1600 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.79 % Allowed : 16.51 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.23), residues: 1300 helix: 2.30 (0.19), residues: 778 sheet: -0.01 (0.41), residues: 158 loop : -0.66 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 490 HIS 0.005 0.001 HIS A 459 PHE 0.012 0.001 PHE B1052 TYR 0.010 0.001 TYR B 440 ARG 0.002 0.000 ARG B1112 *********************** 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: 26 poor density : 136 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7761 (mm-40) REVERT: A 832 ASN cc_start: 0.7038 (OUTLIER) cc_final: 0.6585 (m-40) REVERT: A 850 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8164 (t80) REVERT: A 1073 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7510 (mt) REVERT: A 1112 ARG cc_start: 0.8002 (mtm180) cc_final: 0.7686 (mtm110) REVERT: B 653 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8374 (tp30) REVERT: B 1070 MET cc_start: 0.8442 (tmm) cc_final: 0.7786 (tmm) REVERT: B 1112 ARG cc_start: 0.8053 (mtm110) cc_final: 0.7718 (mtm110) outliers start: 26 outliers final: 21 residues processed: 155 average time/residue: 0.1700 time to fit residues: 41.0101 Evaluate side-chains 153 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 563 VAL Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10134 Z= 0.138 Angle : 0.459 8.597 13830 Z= 0.242 Chirality : 0.039 0.153 1636 Planarity : 0.003 0.029 1708 Dihedral : 9.023 77.520 1600 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.79 % Allowed : 16.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.24), residues: 1300 helix: 2.38 (0.19), residues: 778 sheet: 0.05 (0.41), residues: 162 loop : -0.57 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 490 HIS 0.005 0.001 HIS B 459 PHE 0.020 0.001 PHE B 569 TYR 0.012 0.001 TYR B 827 ARG 0.002 0.000 ARG A 583 *********************** 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 168 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7774 (mm-40) REVERT: A 832 ASN cc_start: 0.6993 (OUTLIER) cc_final: 0.6537 (m-40) REVERT: A 850 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8246 (t80) REVERT: A 1073 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7359 (mt) REVERT: A 1112 ARG cc_start: 0.8002 (mtm180) cc_final: 0.7716 (mtm180) REVERT: B 427 GLN cc_start: 0.9097 (pm20) cc_final: 0.8808 (pm20) REVERT: B 653 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8353 (tp30) REVERT: B 1070 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7832 (tmm) REVERT: B 1112 ARG cc_start: 0.8006 (mtm110) cc_final: 0.7685 (mtm110) outliers start: 26 outliers final: 17 residues processed: 156 average time/residue: 0.1561 time to fit residues: 38.4735 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 : 1.174 ------------------------------------------------------------------------------- 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 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 495 VAL 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 1070 MET Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 80 optimal weight: 30.0000 chunk 86 optimal weight: 0.0370 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.9460 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10134 Z= 0.150 Angle : 0.464 8.839 13830 Z= 0.245 Chirality : 0.038 0.150 1636 Planarity : 0.003 0.031 1708 Dihedral : 8.762 73.539 1600 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.00 % Allowed : 17.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.24), residues: 1300 helix: 2.39 (0.19), residues: 780 sheet: 0.07 (0.40), residues: 162 loop : -0.54 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 490 HIS 0.004 0.001 HIS A 459 PHE 0.016 0.001 PHE B 569 TYR 0.011 0.001 TYR A1067 ARG 0.001 0.000 ARG B1112 *********************** 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 175 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7712 (mm-40) REVERT: A 738 ARG cc_start: 0.8432 (ptm-80) cc_final: 0.8095 (ptm-80) REVERT: A 832 ASN cc_start: 0.7016 (OUTLIER) cc_final: 0.6568 (m-40) REVERT: A 850 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8208 (t80) REVERT: A 1073 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7320 (mt) REVERT: A 1112 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7669 (mtm180) REVERT: B 427 GLN cc_start: 0.9065 (pm20) cc_final: 0.8775 (pm20) REVERT: B 653 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8335 (tp30) REVERT: B 738 ARG cc_start: 0.8249 (ptm-80) cc_final: 0.7879 (ptm-80) REVERT: B 832 ASN cc_start: 0.6976 (OUTLIER) cc_final: 0.6629 (m-40) REVERT: B 1070 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7821 (tmm) REVERT: B 1089 LEU cc_start: 0.8271 (mm) cc_final: 0.7968 (mm) REVERT: B 1112 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7736 (mtm180) outliers start: 28 outliers final: 19 residues processed: 167 average time/residue: 0.1661 time to fit residues: 43.0429 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 : 1.162 ------------------------------------------------------------------------------- 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 495 VAL 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 832 ASN Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 107 optimal weight: 0.0070 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10134 Z= 0.161 Angle : 0.466 8.561 13830 Z= 0.246 Chirality : 0.039 0.151 1636 Planarity : 0.003 0.027 1708 Dihedral : 8.568 69.252 1600 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.00 % Allowed : 18.22 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.24), residues: 1300 helix: 2.41 (0.19), residues: 780 sheet: -0.01 (0.41), residues: 162 loop : -0.52 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 806 HIS 0.004 0.001 HIS B 459 PHE 0.016 0.001 PHE B 569 TYR 0.009 0.001 TYR B 827 ARG 0.004 0.000 ARG B 464 *********************** 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 167 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7772 (mm-40) REVERT: A 738 ARG cc_start: 0.8445 (ptm-80) cc_final: 0.8078 (ptm-80) REVERT: A 832 ASN cc_start: 0.7024 (OUTLIER) cc_final: 0.6595 (m-40) REVERT: A 850 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8224 (t80) REVERT: A 1073 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7271 (mt) REVERT: A 1112 ARG cc_start: 0.7991 (mtm180) cc_final: 0.7674 (mtm180) REVERT: B 427 GLN cc_start: 0.9072 (pm20) cc_final: 0.8780 (pm20) REVERT: B 653 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8336 (tp30) REVERT: B 738 ARG cc_start: 0.8278 (ptm-80) cc_final: 0.7925 (ptm-80) REVERT: B 832 ASN cc_start: 0.7040 (OUTLIER) cc_final: 0.6663 (m-40) REVERT: B 1070 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7838 (tmm) REVERT: B 1112 ARG cc_start: 0.8041 (mtm110) cc_final: 0.7733 (mtm180) outliers start: 28 outliers final: 21 residues processed: 160 average time/residue: 0.1723 time to fit residues: 42.1730 Evaluate side-chains 164 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 814 LEU Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 VAL 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 832 ASN Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.0980 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 80 optimal weight: 0.0470 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 overall best weight: 0.3678 ------------------------------------------------------------------------------- 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 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10134 Z= 0.125 Angle : 0.459 8.666 13830 Z= 0.240 Chirality : 0.038 0.147 1636 Planarity : 0.003 0.026 1708 Dihedral : 8.355 69.766 1600 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.47 % Allowed : 18.33 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.24), residues: 1300 helix: 2.44 (0.19), residues: 782 sheet: 0.06 (0.41), residues: 162 loop : -0.44 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 490 HIS 0.004 0.001 HIS A 459 PHE 0.014 0.001 PHE B 569 TYR 0.010 0.001 TYR B 827 ARG 0.003 0.000 ARG B 464 ********************** 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 177 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 507 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 738 ARG cc_start: 0.8376 (ptm-80) cc_final: 0.8032 (ptm-80) REVERT: A 799 PHE cc_start: 0.8394 (t80) cc_final: 0.8003 (t80) REVERT: A 814 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8335 (tp) REVERT: A 832 ASN cc_start: 0.6985 (OUTLIER) cc_final: 0.6549 (m-40) REVERT: A 850 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8320 (t80) REVERT: A 1073 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7168 (mt) REVERT: A 1112 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7668 (mtm180) REVERT: B 427 GLN cc_start: 0.9088 (pm20) cc_final: 0.8804 (pm20) REVERT: B 507 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7709 (tm-30) REVERT: B 606 MET cc_start: 0.8044 (mmp) cc_final: 0.7653 (mmm) REVERT: B 653 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8449 (tp30) REVERT: B 738 ARG cc_start: 0.8135 (ptm-80) cc_final: 0.7721 (ptm-80) REVERT: B 799 PHE cc_start: 0.8357 (t80) cc_final: 0.7872 (t80) REVERT: B 832 ASN cc_start: 0.7026 (OUTLIER) cc_final: 0.6666 (m-40) REVERT: B 1070 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7854 (tmm) REVERT: B 1073 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7442 (mt) REVERT: B 1112 ARG cc_start: 0.8015 (mtm110) cc_final: 0.7709 (mtm180) outliers start: 23 outliers final: 15 residues processed: 171 average time/residue: 0.1683 time to fit residues: 43.8127 Evaluate side-chains 166 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 495 VAL Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.130580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.103552 restraints weight = 19917.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.107054 restraints weight = 9849.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.109332 restraints weight = 6314.980| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3896 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= 0.189 Angle : 0.482 8.126 13830 Z= 0.254 Chirality : 0.039 0.149 1636 Planarity : 0.003 0.028 1708 Dihedral : 8.039 66.517 1598 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.68 % Allowed : 18.22 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.24), residues: 1300 helix: 2.47 (0.19), residues: 780 sheet: -0.04 (0.41), residues: 162 loop : -0.46 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 490 HIS 0.004 0.001 HIS A 536 PHE 0.017 0.001 PHE B 569 TYR 0.010 0.001 TYR B 827 ARG 0.004 0.000 ARG B 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1798.58 seconds wall clock time: 33 minutes 49.91 seconds (2029.91 seconds total)