Starting phenix.real_space_refine on Tue Sep 24 04:19:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi0_32517/09_2024/7wi0_32517.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi0_32517/09_2024/7wi0_32517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi0_32517/09_2024/7wi0_32517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi0_32517/09_2024/7wi0_32517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi0_32517/09_2024/7wi0_32517.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi0_32517/09_2024/7wi0_32517.cif" } resolution = 3.82 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= 0.012 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4303 2.51 5 N 1148 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6823 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "B" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 940 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 935 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.52, per 1000 atoms: 0.81 Number of scatterers: 6823 At special positions: 0 Unit cell: (86.358, 94.916, 122.146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1342 8.00 N 1148 7.00 C 4303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.01 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 929.7 milliseconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 22 sheets defined 2.7% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.848A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 removed outlier: 3.620A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.563A pdb=" N ASP C 90 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.807A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.726A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.608A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.636A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.689A pdb=" N LEU B 18 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP B 73 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 80 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 6 through 7 removed outlier: 3.508A pdb=" N LEU C 18 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR C 69 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 7.932A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.722A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB3, first strand: chain 'D' and resid 53 through 54 removed outlier: 5.405A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN D 38 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.603A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.674A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.522A pdb=" N GLN E 37 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN E 89 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR E 85 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.909A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.054A pdb=" N GLU H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL H 119 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA H 92 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 18 through 19 removed outlier: 3.506A pdb=" N ASP H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 72 through 73 removed outlier: 3.561A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.646A pdb=" N TYR L 88 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL L 107 " --> pdb=" O ALA L 86 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA L 86 " --> pdb=" O VAL L 107 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.646A pdb=" N TYR L 88 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL L 107 " --> pdb=" O ALA L 86 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA L 86 " --> pdb=" O VAL L 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER L 92 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL L 100 " --> pdb=" O SER L 92 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 17 through 21 158 hydrogen bonds defined for protein. 384 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: 1.77 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1101 1.26 - 1.40: 1858 1.40 - 1.54: 3952 1.54 - 1.68: 39 1.68 - 1.83: 40 Bond restraints: 6990 Sorted by residual: bond pdb=" C THR C 78 " pdb=" O THR C 78 " ideal model delta sigma weight residual 1.234 1.462 -0.228 1.22e-02 6.72e+03 3.49e+02 bond pdb=" C SER B 106 " pdb=" O SER B 106 " ideal model delta sigma weight residual 1.234 1.117 0.117 1.19e-02 7.06e+03 9.66e+01 bond pdb=" C VAL B 101 " pdb=" O VAL B 101 " ideal model delta sigma weight residual 1.235 1.150 0.084 1.45e-02 4.76e+03 3.38e+01 bond pdb=" CA SER B 106 " pdb=" C SER B 106 " ideal model delta sigma weight residual 1.521 1.452 0.069 1.22e-02 6.72e+03 3.22e+01 bond pdb=" C THR C 78 " pdb=" N LEU C 79 " ideal model delta sigma weight residual 1.331 1.401 -0.070 1.29e-02 6.01e+03 2.94e+01 ... (remaining 6985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 9380 3.67 - 7.34: 101 7.34 - 11.01: 15 11.01 - 14.68: 1 14.68 - 18.36: 2 Bond angle restraints: 9499 Sorted by residual: angle pdb=" N GLY B 105 " pdb=" CA GLY B 105 " pdb=" C GLY B 105 " ideal model delta sigma weight residual 112.49 130.85 -18.36 1.21e+00 6.83e-01 2.30e+02 angle pdb=" N VAL B 101 " pdb=" CA VAL B 101 " pdb=" C VAL B 101 " ideal model delta sigma weight residual 112.29 121.27 -8.98 9.40e-01 1.13e+00 9.12e+01 angle pdb=" N ASP B 112 " pdb=" CA ASP B 112 " pdb=" C ASP B 112 " ideal model delta sigma weight residual 111.36 120.42 -9.06 1.09e+00 8.42e-01 6.91e+01 angle pdb=" N ALA B 102 " pdb=" CA ALA B 102 " pdb=" C ALA B 102 " ideal model delta sigma weight residual 109.59 98.35 11.24 1.47e+00 4.63e-01 5.85e+01 angle pdb=" O SER B 106 " pdb=" C SER B 106 " pdb=" N SER B 107 " ideal model delta sigma weight residual 123.46 116.86 6.60 9.90e-01 1.02e+00 4.44e+01 ... (remaining 9494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3694 17.97 - 35.95: 350 35.95 - 53.92: 53 53.92 - 71.89: 9 71.89 - 89.87: 8 Dihedral angle restraints: 4114 sinusoidal: 1576 harmonic: 2538 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 149.43 -56.43 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CA SER E 93 " pdb=" C SER E 93 " pdb=" N TYR E 94 " pdb=" CA TYR E 94 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual -86.00 -121.59 35.59 1 1.00e+01 1.00e-02 1.79e+01 ... (remaining 4111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 916 0.095 - 0.189: 97 0.189 - 0.284: 13 0.284 - 0.379: 1 0.379 - 0.474: 1 Chirality restraints: 1028 Sorted by residual: chirality pdb=" CA VAL B 101 " pdb=" N VAL B 101 " pdb=" C VAL B 101 " pdb=" CB VAL B 101 " both_signs ideal model delta sigma weight residual False 2.44 1.97 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CA SER B 107 " pdb=" N SER B 107 " pdb=" C SER B 107 " pdb=" CB SER B 107 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA TYR E 94 " pdb=" N TYR E 94 " pdb=" C TYR E 94 " pdb=" CB TYR E 94 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1025 not shown) Planarity restraints: 1227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 77 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C ASN C 77 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN C 77 " 0.018 2.00e-02 2.50e+03 pdb=" N THR C 78 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " 0.043 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 373 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO L 46 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " 0.035 5.00e-02 4.00e+02 ... (remaining 1224 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1858 2.79 - 3.32: 5543 3.32 - 3.85: 10966 3.85 - 4.37: 11967 4.37 - 4.90: 21668 Nonbonded interactions: 52002 Sorted by model distance: nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 117 " model vdw 2.265 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.272 3.040 nonbonded pdb=" OG SER D 63 " pdb=" O THR D 74 " model vdw 2.314 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.315 3.040 nonbonded pdb=" OD1 ASP B 90 " pdb=" OH TYR B 94 " model vdw 2.317 3.040 ... (remaining 51997 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 'D' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) selection = (chain 'E' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) } 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=0.50 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.100 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.008 0.228 6990 Z= 0.528 Angle : 1.048 18.355 9499 Z= 0.635 Chirality : 0.064 0.474 1028 Planarity : 0.007 0.064 1226 Dihedral : 14.368 89.866 2487 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.60 % Favored : 91.28 % Rotamer: Outliers : 0.40 % Allowed : 10.08 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -4.32 (0.24), residues: 872 helix: -5.25 (0.15), residues: 30 sheet: -2.73 (0.25), residues: 349 loop : -2.85 (0.23), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 114 HIS 0.005 0.002 HIS L 36 PHE 0.019 0.002 PHE B 27 TYR 0.023 0.002 TYR C 95 ARG 0.005 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 226 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7452 (ttpt) REVERT: B 50 VAL cc_start: 0.9168 (p) cc_final: 0.8790 (p) REVERT: B 51 MET cc_start: 0.8872 (mmm) cc_final: 0.8489 (mmt) REVERT: B 116 GLN cc_start: 0.8414 (tp40) cc_final: 0.8191 (mm-40) REVERT: C 65 LYS cc_start: 0.7983 (ptpt) cc_final: 0.7657 (ttpt) REVERT: E 2 ILE cc_start: 0.7706 (mp) cc_final: 0.7208 (mp) REVERT: E 85 THR cc_start: 0.8060 (t) cc_final: 0.7840 (m) REVERT: E 90 GLN cc_start: 0.8712 (pp30) cc_final: 0.8374 (pp30) REVERT: H 62 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8251 (tm-30) REVERT: H 89 GLU cc_start: 0.7658 (mp0) cc_final: 0.7446 (mt-10) REVERT: L 63 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7772 (mtp-110) outliers start: 3 outliers final: 1 residues processed: 227 average time/residue: 0.2065 time to fit residues: 60.2543 Evaluate side-chains 167 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN B 39 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS D 31 ASN D 38 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN L 1 GLN L 36 HIS L 39 GLN L 40 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6990 Z= 0.233 Angle : 0.645 7.658 9499 Z= 0.343 Chirality : 0.046 0.205 1028 Planarity : 0.005 0.050 1226 Dihedral : 5.528 38.983 1001 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.15 % Allowed : 19.22 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -3.53 (0.26), residues: 872 helix: -5.02 (0.20), residues: 18 sheet: -2.29 (0.26), residues: 347 loop : -2.29 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 47 HIS 0.003 0.001 HIS H 107 PHE 0.021 0.002 PHE B 29 TYR 0.026 0.002 TYR L 51 ARG 0.004 0.001 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 196 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8333 (t60) cc_final: 0.7792 (t60) REVERT: C 36 TRP cc_start: 0.7864 (m100) cc_final: 0.7530 (m100) REVERT: C 45 LEU cc_start: 0.8462 (mt) cc_final: 0.8242 (mt) REVERT: C 65 LYS cc_start: 0.7977 (ptpt) cc_final: 0.7637 (ttpt) REVERT: E 78 LEU cc_start: 0.7959 (mm) cc_final: 0.7712 (tt) REVERT: E 90 GLN cc_start: 0.8743 (pp30) cc_final: 0.8324 (pp30) REVERT: H 43 GLN cc_start: 0.8546 (mp10) cc_final: 0.8055 (mp10) REVERT: H 87 ARG cc_start: 0.6864 (mtm110) cc_final: 0.6515 (mtm110) REVERT: L 63 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7515 (ttp-110) outliers start: 16 outliers final: 5 residues processed: 204 average time/residue: 0.1372 time to fit residues: 37.1586 Evaluate side-chains 177 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 172 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN H 62 GLN L 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6990 Z= 0.241 Angle : 0.642 7.501 9499 Z= 0.336 Chirality : 0.045 0.207 1028 Planarity : 0.005 0.052 1226 Dihedral : 5.119 35.319 996 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.96 % Allowed : 20.70 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -3.23 (0.27), residues: 872 helix: -5.06 (0.18), residues: 24 sheet: -2.13 (0.26), residues: 362 loop : -1.96 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 47 HIS 0.004 0.001 HIS L 36 PHE 0.015 0.001 PHE A 490 TYR 0.023 0.001 TYR E 94 ARG 0.004 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 180 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8251 (t60) cc_final: 0.7636 (t60) REVERT: C 36 TRP cc_start: 0.7813 (m100) cc_final: 0.7581 (m100) REVERT: C 45 LEU cc_start: 0.8482 (mt) cc_final: 0.8250 (mt) REVERT: C 65 LYS cc_start: 0.8020 (ptpt) cc_final: 0.7723 (ttpt) REVERT: C 86 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7752 (pp) REVERT: E 81 ASP cc_start: 0.7678 (t0) cc_final: 0.7443 (t0) REVERT: E 90 GLN cc_start: 0.8731 (pp30) cc_final: 0.8314 (pp30) REVERT: H 43 GLN cc_start: 0.8584 (mp10) cc_final: 0.8120 (mp10) REVERT: L 63 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7600 (mtp-110) outliers start: 22 outliers final: 16 residues processed: 191 average time/residue: 0.1877 time to fit residues: 47.1712 Evaluate side-chains 184 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 0.1980 chunk 74 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN D 90 GLN E 100 GLN L 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6990 Z= 0.168 Angle : 0.611 9.220 9499 Z= 0.312 Chirality : 0.043 0.163 1028 Planarity : 0.004 0.050 1226 Dihedral : 4.745 29.232 996 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.69 % Allowed : 22.85 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.92 (0.28), residues: 872 helix: -5.02 (0.19), residues: 24 sheet: -1.75 (0.27), residues: 366 loop : -1.88 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 47 HIS 0.004 0.001 HIS A 519 PHE 0.027 0.001 PHE B 29 TYR 0.021 0.001 TYR E 94 ARG 0.005 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8091 (t60) cc_final: 0.7719 (t60) REVERT: C 45 LEU cc_start: 0.8460 (mt) cc_final: 0.8199 (mt) REVERT: C 65 LYS cc_start: 0.8008 (ptpt) cc_final: 0.7695 (ttpt) REVERT: C 72 ARG cc_start: 0.7534 (ptp-170) cc_final: 0.7333 (ptm160) REVERT: C 86 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7841 (pp) REVERT: E 81 ASP cc_start: 0.7627 (t0) cc_final: 0.7286 (t0) REVERT: E 90 GLN cc_start: 0.8631 (pp30) cc_final: 0.8322 (pp30) REVERT: H 43 GLN cc_start: 0.8555 (mp10) cc_final: 0.8189 (mp10) REVERT: H 48 MET cc_start: 0.7858 (mtt) cc_final: 0.7579 (mtp) REVERT: H 63 LYS cc_start: 0.8659 (tttp) cc_final: 0.8337 (ttpp) REVERT: L 63 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7608 (mtp-110) outliers start: 20 outliers final: 10 residues processed: 185 average time/residue: 0.1940 time to fit residues: 46.8383 Evaluate side-chains 176 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 93 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6990 Z= 0.322 Angle : 0.680 10.280 9499 Z= 0.350 Chirality : 0.046 0.246 1028 Planarity : 0.005 0.057 1226 Dihedral : 5.055 32.420 996 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 4.30 % Allowed : 23.12 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.81 (0.28), residues: 872 helix: -5.11 (0.20), residues: 30 sheet: -1.70 (0.27), residues: 367 loop : -1.72 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 47 HIS 0.005 0.002 HIS C 35 PHE 0.030 0.002 PHE B 29 TYR 0.014 0.002 TYR H 60 ARG 0.003 0.001 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8241 (t60) cc_final: 0.7828 (t60) REVERT: B 109 ASP cc_start: 0.8328 (t70) cc_final: 0.8122 (t70) REVERT: C 65 LYS cc_start: 0.8015 (ptpt) cc_final: 0.7772 (ttpt) REVERT: E 81 ASP cc_start: 0.7591 (t0) cc_final: 0.7229 (t0) REVERT: E 90 GLN cc_start: 0.8748 (pp30) cc_final: 0.8243 (pp30) REVERT: H 43 GLN cc_start: 0.8605 (mp10) cc_final: 0.8224 (mp10) REVERT: H 87 ARG cc_start: 0.7052 (mtm110) cc_final: 0.6840 (mtm110) REVERT: L 63 ARG cc_start: 0.8079 (mtm-85) cc_final: 0.7450 (mtp-110) outliers start: 32 outliers final: 25 residues processed: 184 average time/residue: 0.1847 time to fit residues: 45.0245 Evaluate side-chains 182 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6990 Z= 0.223 Angle : 0.648 8.448 9499 Z= 0.330 Chirality : 0.044 0.203 1028 Planarity : 0.004 0.047 1226 Dihedral : 4.900 30.653 996 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.76 % Allowed : 25.13 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.62 (0.28), residues: 872 helix: -4.74 (0.33), residues: 18 sheet: -1.60 (0.27), residues: 374 loop : -1.68 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 36 HIS 0.004 0.001 HIS C 35 PHE 0.015 0.001 PHE A 490 TYR 0.022 0.001 TYR E 94 ARG 0.004 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8121 (t60) cc_final: 0.7788 (t60) REVERT: C 5 VAL cc_start: 0.7898 (t) cc_final: 0.7669 (t) REVERT: C 65 LYS cc_start: 0.8021 (ptpt) cc_final: 0.7762 (ttpt) REVERT: C 86 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8108 (pp) REVERT: E 37 GLN cc_start: 0.7023 (tt0) cc_final: 0.6738 (tt0) REVERT: E 81 ASP cc_start: 0.7560 (t0) cc_final: 0.7305 (t0) REVERT: E 90 GLN cc_start: 0.8699 (pp30) cc_final: 0.8151 (pp30) REVERT: H 43 GLN cc_start: 0.8565 (mp10) cc_final: 0.8264 (mp10) REVERT: L 63 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7488 (ttp-110) REVERT: L 81 GLN cc_start: 0.8510 (mp10) cc_final: 0.8259 (mp10) outliers start: 28 outliers final: 20 residues processed: 186 average time/residue: 0.1872 time to fit residues: 46.0810 Evaluate side-chains 179 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6990 Z= 0.227 Angle : 0.667 10.102 9499 Z= 0.339 Chirality : 0.044 0.202 1028 Planarity : 0.004 0.053 1226 Dihedral : 4.917 29.746 996 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.63 % Allowed : 24.87 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.56 (0.28), residues: 872 helix: -4.87 (0.25), residues: 24 sheet: -1.54 (0.27), residues: 374 loop : -1.59 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 36 HIS 0.004 0.001 HIS C 35 PHE 0.015 0.001 PHE A 490 TYR 0.018 0.001 TYR E 94 ARG 0.004 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8102 (t60) cc_final: 0.7805 (t60) REVERT: C 86 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8147 (pp) REVERT: E 90 GLN cc_start: 0.8792 (pp30) cc_final: 0.8362 (pp30) REVERT: H 43 GLN cc_start: 0.8542 (mp10) cc_final: 0.8290 (mp10) REVERT: L 63 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7538 (ttp-110) outliers start: 27 outliers final: 23 residues processed: 176 average time/residue: 0.1813 time to fit residues: 42.5431 Evaluate side-chains 179 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 0.0170 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6990 Z= 0.218 Angle : 0.663 11.042 9499 Z= 0.338 Chirality : 0.044 0.194 1028 Planarity : 0.004 0.047 1226 Dihedral : 4.856 28.560 996 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.90 % Allowed : 25.13 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.44 (0.28), residues: 872 helix: -4.82 (0.27), residues: 24 sheet: -1.44 (0.27), residues: 374 loop : -1.53 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 36 HIS 0.004 0.001 HIS C 35 PHE 0.013 0.001 PHE A 490 TYR 0.020 0.001 TYR E 94 ARG 0.007 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8057 (t60) cc_final: 0.7811 (t60) REVERT: C 86 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8147 (pp) REVERT: E 90 GLN cc_start: 0.8777 (pp30) cc_final: 0.8349 (pp30) REVERT: H 43 GLN cc_start: 0.8540 (mp10) cc_final: 0.8286 (mp10) REVERT: H 89 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8077 (pt0) REVERT: L 63 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7534 (ttp-110) outliers start: 29 outliers final: 24 residues processed: 179 average time/residue: 0.1857 time to fit residues: 44.2071 Evaluate side-chains 179 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 23 optimal weight: 0.0170 chunk 69 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN E 37 GLN E 79 GLN H 108 ASN L 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6990 Z= 0.192 Angle : 0.648 9.139 9499 Z= 0.329 Chirality : 0.044 0.181 1028 Planarity : 0.004 0.051 1226 Dihedral : 4.725 26.169 996 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 2.96 % Allowed : 26.61 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.27 (0.29), residues: 872 helix: -4.90 (0.22), residues: 18 sheet: -1.34 (0.27), residues: 373 loop : -1.45 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 36 HIS 0.003 0.001 HIS C 35 PHE 0.012 0.001 PHE A 490 TYR 0.019 0.001 TYR E 94 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7240 (mt-10) REVERT: C 86 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8119 (pp) REVERT: E 90 GLN cc_start: 0.8708 (pp30) cc_final: 0.8165 (pp30) REVERT: H 43 GLN cc_start: 0.8529 (mp10) cc_final: 0.8283 (mp10) REVERT: L 63 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7553 (ttp-110) outliers start: 22 outliers final: 17 residues processed: 171 average time/residue: 0.1821 time to fit residues: 41.7123 Evaluate side-chains 169 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 93 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 0.0470 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 ASN L 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6990 Z= 0.251 Angle : 0.687 10.414 9499 Z= 0.347 Chirality : 0.045 0.206 1028 Planarity : 0.004 0.049 1226 Dihedral : 4.879 27.142 996 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 2.96 % Allowed : 26.48 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.30 (0.28), residues: 872 helix: -4.85 (0.24), residues: 18 sheet: -1.28 (0.28), residues: 352 loop : -1.56 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 47 HIS 0.004 0.001 HIS C 35 PHE 0.014 0.001 PHE A 490 TYR 0.018 0.002 TYR E 94 ARG 0.006 0.000 ARG L 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7297 (mt-10) REVERT: B 47 TRP cc_start: 0.8217 (t60) cc_final: 0.7835 (t60) REVERT: C 86 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8122 (pp) REVERT: E 90 GLN cc_start: 0.8777 (pp30) cc_final: 0.8331 (pp30) REVERT: H 43 GLN cc_start: 0.8529 (mp10) cc_final: 0.8278 (mp10) outliers start: 22 outliers final: 21 residues processed: 167 average time/residue: 0.1774 time to fit residues: 40.0049 Evaluate side-chains 174 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 93 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 18 optimal weight: 0.3980 chunk 68 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN E 79 GLN L 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.124703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102148 restraints weight = 11782.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105150 restraints weight = 6867.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107251 restraints weight = 4772.290| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6990 Z= 0.222 Angle : 0.688 12.217 9499 Z= 0.347 Chirality : 0.044 0.195 1028 Planarity : 0.004 0.051 1226 Dihedral : 4.848 26.390 996 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.36 % Allowed : 26.75 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.24 (0.28), residues: 872 helix: -4.85 (0.24), residues: 18 sheet: -1.26 (0.28), residues: 359 loop : -1.50 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 47 HIS 0.003 0.001 HIS C 35 PHE 0.055 0.002 PHE C 68 TYR 0.019 0.001 TYR E 94 ARG 0.008 0.001 ARG H 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1994.36 seconds wall clock time: 40 minutes 5.46 seconds (2405.46 seconds total)