Starting phenix.real_space_refine on Fri Jul 25 17:05:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fbi_31515/07_2025/7fbi_31515.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fbi_31515/07_2025/7fbi_31515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fbi_31515/07_2025/7fbi_31515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fbi_31515/07_2025/7fbi_31515.map" model { file = "/net/cci-nas-00/data/ceres_data/7fbi_31515/07_2025/7fbi_31515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fbi_31515/07_2025/7fbi_31515.cif" } resolution = 3.9 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= 0.002 sd= 0.906 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 39 5.16 5 C 4895 2.51 5 N 1310 2.21 5 O 1533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7777 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 798 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 812 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "A" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4467 Classifications: {'peptide': 557} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 540} Chain breaks: 3 Chain: "M" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 819 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "N" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 881 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Time building chain proxies: 4.94, per 1000 atoms: 0.64 Number of scatterers: 7777 At special positions: 0 Unit cell: (69.3, 158.4, 192.5, 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 39 16.00 O 1533 8.00 N 1310 7.00 C 4895 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 93 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 20 sheets defined 9.7% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.165A pdb=" N SER H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR H 32 " --> pdb=" O LEU H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'A' and resid 128 through 132 removed outlier: 3.720A pdb=" N GLU A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 132 " --> pdb=" O SER A 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 132' Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.984A pdb=" N ILE A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.822A pdb=" N LYS A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 467 removed outlier: 3.919A pdb=" N ALA A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 476 Processing helix chain 'A' and resid 480 through 497 removed outlier: 3.633A pdb=" N CYS A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 496 " --> pdb=" O MET A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 511 removed outlier: 4.196A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER A 507 " --> pdb=" O THR A 503 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 645 through 651 removed outlier: 3.915A pdb=" N ARG A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 651 " --> pdb=" O ASP A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 665 removed outlier: 3.981A pdb=" N PHE A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG A 662 " --> pdb=" O GLU A 658 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.530A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN H 39 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 23 through 24 removed outlier: 3.592A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR L 74 " --> pdb=" O ARG L 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.929A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.929A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN L 38 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA7, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.749A pdb=" N GLY A 80 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR A 306 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 311 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 314 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA9, first strand: chain 'A' and resid 120 through 125 removed outlier: 3.643A pdb=" N ASN A 105 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 94 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 213 " --> pdb=" O PHE A 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.661A pdb=" N ALA A 213 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 94 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 277 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 145 through 149 removed outlier: 4.072A pdb=" N VAL A 145 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR A 156 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 147 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 370 through 373 removed outlier: 3.796A pdb=" N THR A 370 " --> pdb=" O TRP A 382 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP A 382 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 372 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 551 through 552 Processing sheet with id=AB5, first strand: chain 'A' and resid 556 through 560 removed outlier: 3.574A pdb=" N GLN A 571 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 579 " --> pdb=" O GLN A 571 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 594 through 598 removed outlier: 3.680A pdb=" N TYR A 594 " --> pdb=" O TYR A 605 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 605 " --> pdb=" O TYR A 594 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A 596 " --> pdb=" O HIS A 603 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS A 603 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 601 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 612 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 4 through 6 removed outlier: 3.675A pdb=" N ILE M 21 " --> pdb=" O LEU M 73 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N CYS M 23 " --> pdb=" O TYR M 71 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TYR M 71 " --> pdb=" O CYS M 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER M 67 " --> pdb=" O ASP M 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 35 through 38 removed outlier: 3.744A pdb=" N TYR M 87 " --> pdb=" O TYR M 36 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG M 38 " --> pdb=" O THR M 85 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR M 85 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.592A pdb=" N THR N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL N 76 " --> pdb=" O CYS N 22 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP N 77 " --> pdb=" O SER N 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 18 through 19 removed outlier: 3.571A pdb=" N MET N 80 " --> pdb=" O LEU N 18 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 33 through 39 removed outlier: 4.501A pdb=" N GLU N 33 " --> pdb=" O GLY N 96 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL N 37 " --> pdb=" O PHE N 92 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN N 39 " --> pdb=" O THR N 90 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR N 90 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR N 114 " --> pdb=" O TYR N 91 " (cutoff:3.500A) 125 hydrogen bonds defined for protein. 318 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: 1.71 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1273 1.31 - 1.44: 2253 1.44 - 1.57: 4352 1.57 - 1.70: 2 1.70 - 1.83: 58 Bond restraints: 7938 Sorted by residual: bond pdb=" N HIS A 352 " pdb=" CA HIS A 352 " ideal model delta sigma weight residual 1.459 1.375 0.085 1.18e-02 7.18e+03 5.16e+01 bond pdb=" CA ARG H 10 " pdb=" C ARG H 10 " ideal model delta sigma weight residual 1.523 1.598 -0.075 1.34e-02 5.57e+03 3.16e+01 bond pdb=" C SER M 93 " pdb=" O SER M 93 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.26e-02 6.30e+03 2.07e+01 bond pdb=" CA PHE M 92 " pdb=" C PHE M 92 " ideal model delta sigma weight residual 1.531 1.481 0.050 1.12e-02 7.97e+03 2.02e+01 bond pdb=" C HIS A 352 " pdb=" N GLU A 353 " ideal model delta sigma weight residual 1.335 1.279 0.056 1.27e-02 6.20e+03 1.92e+01 ... (remaining 7933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 10574 3.59 - 7.18: 163 7.18 - 10.77: 26 10.77 - 14.36: 5 14.36 - 17.95: 2 Bond angle restraints: 10770 Sorted by residual: angle pdb=" N SER M 95 " pdb=" CA SER M 95 " pdb=" C SER M 95 " ideal model delta sigma weight residual 109.24 127.19 -17.95 1.51e+00 4.39e-01 1.41e+02 angle pdb=" C MET A 351 " pdb=" N HIS A 352 " pdb=" CA HIS A 352 " ideal model delta sigma weight residual 120.63 108.66 11.97 1.36e+00 5.41e-01 7.75e+01 angle pdb=" N GLN M 90 " pdb=" CA GLN M 90 " pdb=" C GLN M 90 " ideal model delta sigma weight residual 112.59 122.19 -9.60 1.22e+00 6.72e-01 6.19e+01 angle pdb=" N GLY M 91 " pdb=" CA GLY M 91 " pdb=" C GLY M 91 " ideal model delta sigma weight residual 111.34 125.65 -14.31 1.82e+00 3.02e-01 6.18e+01 angle pdb=" N PHE M 92 " pdb=" CA PHE M 92 " pdb=" C PHE M 92 " ideal model delta sigma weight residual 110.70 120.15 -9.45 1.55e+00 4.16e-01 3.72e+01 ... (remaining 10765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 4054 16.60 - 33.20: 500 33.20 - 49.79: 93 49.79 - 66.39: 19 66.39 - 82.99: 13 Dihedral angle restraints: 4679 sinusoidal: 1799 harmonic: 2880 Sorted by residual: dihedral pdb=" CA TRP N 47 " pdb=" C TRP N 47 " pdb=" N ILE N 48 " pdb=" CA ILE N 48 " ideal model delta harmonic sigma weight residual 180.00 -119.15 -60.85 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA TYR N 106 " pdb=" C TYR N 106 " pdb=" N PHE N 107 " pdb=" CA PHE N 107 " ideal model delta harmonic sigma weight residual 180.00 135.46 44.54 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" N SER M 95 " pdb=" C SER M 95 " pdb=" CA SER M 95 " pdb=" CB SER M 95 " ideal model delta harmonic sigma weight residual 122.80 143.24 -20.44 0 2.50e+00 1.60e-01 6.68e+01 ... (remaining 4676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 1206 0.202 - 0.404: 11 0.404 - 0.606: 2 0.606 - 0.807: 0 0.807 - 1.009: 1 Chirality restraints: 1220 Sorted by residual: chirality pdb=" CA SER M 95 " pdb=" N SER M 95 " pdb=" C SER M 95 " pdb=" CB SER M 95 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" CA ARG H 10 " pdb=" N ARG H 10 " pdb=" C ARG H 10 " pdb=" CB ARG H 10 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" CA GLN M 90 " pdb=" N GLN M 90 " pdb=" C GLN M 90 " pdb=" CB GLN M 90 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 ... (remaining 1217 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 352 " 0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C HIS A 352 " -0.069 2.00e-02 2.50e+03 pdb=" O HIS A 352 " 0.027 2.00e-02 2.50e+03 pdb=" N GLU A 353 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 91 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C GLY M 91 " 0.060 2.00e-02 2.50e+03 pdb=" O GLY M 91 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE M 92 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN M 90 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" CD GLN M 90 " 0.051 2.00e-02 2.50e+03 pdb=" OE1 GLN M 90 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 GLN M 90 " -0.017 2.00e-02 2.50e+03 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 262 2.66 - 3.22: 6924 3.22 - 3.78: 11285 3.78 - 4.34: 13074 4.34 - 4.90: 21101 Nonbonded interactions: 52646 Sorted by model distance: nonbonded pdb=" O HIS A 352 " pdb=" N TYR A 355 " model vdw 2.095 3.120 nonbonded pdb=" OE1 GLN M 90 " pdb=" O SER M 100 " model vdw 2.102 3.040 nonbonded pdb=" OG SER M 95 " pdb=" N ASN M 96 " model vdw 2.198 3.120 nonbonded pdb=" N GLN M 90 " pdb=" OE1 GLN M 90 " model vdw 2.217 3.120 nonbonded pdb=" OH TYR A 142 " pdb=" OD1 ASN A 163 " model vdw 2.232 3.040 ... (remaining 52641 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 20.380 Find NCS groups from input model: 0.090 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.007 0.085 7940 Z= 0.357 Angle : 1.182 17.954 10774 Z= 0.659 Chirality : 0.073 1.009 1220 Planarity : 0.007 0.062 1374 Dihedral : 15.514 82.990 2841 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.56 % Favored : 85.34 % Rotamer: Outliers : 0.35 % Allowed : 14.67 % Favored : 84.98 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -5.16 (0.20), residues: 989 helix: -4.53 (0.26), residues: 67 sheet: -3.23 (0.29), residues: 255 loop : -3.61 (0.18), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP N 110 HIS 0.008 0.002 HIS A 603 PHE 0.030 0.002 PHE N 107 TYR 0.032 0.002 TYR M 87 ARG 0.008 0.001 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.35204 ( 114) hydrogen bonds : angle 10.48511 ( 318) SS BOND : bond 0.00837 ( 2) SS BOND : angle 1.32502 ( 4) covalent geometry : bond 0.00684 ( 7938) covalent geometry : angle 1.18184 (10770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 234 time to evaluate : 0.874 Fit side-chains REVERT: H 5 LYS cc_start: 0.9268 (mmmt) cc_final: 0.9061 (mmmt) REVERT: H 29 LEU cc_start: 0.8711 (tt) cc_final: 0.8284 (mm) REVERT: H 79 LYS cc_start: 0.9147 (mmtp) cc_final: 0.8855 (mmtm) REVERT: H 101 MET cc_start: 0.8774 (mmm) cc_final: 0.8122 (mtt) REVERT: L 35 TRP cc_start: 0.7424 (m-10) cc_final: 0.6904 (m-10) REVERT: L 37 GLN cc_start: 0.9440 (tm-30) cc_final: 0.8951 (tm-30) REVERT: L 38 GLN cc_start: 0.9113 (pp30) cc_final: 0.8690 (pm20) REVERT: L 39 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8175 (tppt) REVERT: L 42 GLN cc_start: 0.8744 (mp10) cc_final: 0.8480 (mp10) REVERT: L 55 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7902 (tm-30) REVERT: L 63 ARG cc_start: 0.8525 (ptm160) cc_final: 0.8032 (mtm110) REVERT: L 70 GLU cc_start: 0.8738 (pp20) cc_final: 0.8435 (mt-10) REVERT: L 78 LEU cc_start: 0.8804 (mm) cc_final: 0.8378 (mt) REVERT: L 101 ASN cc_start: 0.8794 (p0) cc_final: 0.8154 (p0) REVERT: A 125 PHE cc_start: 0.8635 (m-10) cc_final: 0.8105 (m-10) REVERT: A 147 MET cc_start: 0.7971 (tmm) cc_final: 0.7299 (tmm) REVERT: A 181 TYR cc_start: 0.7255 (m-80) cc_final: 0.7048 (m-80) REVERT: A 212 MET cc_start: 0.8189 (tpp) cc_final: 0.7910 (tpp) REVERT: A 256 ASN cc_start: 0.9171 (p0) cc_final: 0.8941 (p0) REVERT: A 272 GLU cc_start: 0.8672 (tp30) cc_final: 0.8079 (mt-10) REVERT: A 279 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8276 (mmmm) REVERT: A 313 LYS cc_start: 0.9362 (tppp) cc_final: 0.9033 (tppt) REVERT: A 344 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7332 (mp0) REVERT: A 382 TRP cc_start: 0.6197 (p-90) cc_final: 0.5726 (p-90) REVERT: A 486 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8024 (tm-30) REVERT: A 492 MET cc_start: 0.9320 (tmm) cc_final: 0.9105 (tmm) REVERT: A 568 TYR cc_start: 0.8213 (m-10) cc_final: 0.8004 (m-80) REVERT: A 589 GLN cc_start: 0.8418 (pm20) cc_final: 0.8188 (pm20) REVERT: A 600 ASN cc_start: 0.9005 (t0) cc_final: 0.8575 (t0) REVERT: A 603 HIS cc_start: 0.8715 (p-80) cc_final: 0.8481 (p-80) REVERT: A 609 HIS cc_start: 0.8156 (m90) cc_final: 0.7621 (m90) REVERT: A 635 ASN cc_start: 0.9020 (p0) cc_final: 0.8760 (m-40) REVERT: A 653 ASN cc_start: 0.8909 (t0) cc_final: 0.8258 (t0) REVERT: A 662 ARG cc_start: 0.8798 (ptm-80) cc_final: 0.7945 (ttm170) REVERT: A 663 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8398 (tm-30) REVERT: M 2 LEU cc_start: 0.8616 (pt) cc_final: 0.8386 (pp) REVERT: M 22 LYS cc_start: 0.8271 (pttt) cc_final: 0.8026 (ptpp) REVERT: M 88 CYS cc_start: 0.4654 (p) cc_final: 0.3653 (p) REVERT: M 92 PHE cc_start: 0.4548 (OUTLIER) cc_final: 0.3828 (t80) REVERT: N 22 CYS cc_start: 0.5443 (t) cc_final: 0.5185 (t) REVERT: N 32 TYR cc_start: 0.7378 (m-80) cc_final: 0.5917 (m-80) REVERT: N 34 MET cc_start: 0.9205 (mmp) cc_final: 0.8833 (mmp) REVERT: N 36 TRP cc_start: 0.8163 (m100) cc_final: 0.7632 (m100) REVERT: N 50 THR cc_start: 0.9180 (t) cc_final: 0.8457 (p) REVERT: N 51 ILE cc_start: 0.9253 (tt) cc_final: 0.8866 (tt) outliers start: 3 outliers final: 2 residues processed: 236 average time/residue: 0.2118 time to fit residues: 65.7631 Evaluate side-chains 190 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 187 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 58 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN H 100 ASN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.151543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104555 restraints weight = 15365.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107757 restraints weight = 8535.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.109752 restraints weight = 5804.085| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7940 Z= 0.132 Angle : 0.716 8.882 10774 Z= 0.378 Chirality : 0.045 0.189 1220 Planarity : 0.005 0.057 1374 Dihedral : 7.164 55.582 1105 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 3.84 % Allowed : 18.86 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.52 (0.22), residues: 989 helix: -3.36 (0.40), residues: 70 sheet: -2.62 (0.30), residues: 270 loop : -3.32 (0.20), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 35 HIS 0.002 0.000 HIS A 316 PHE 0.015 0.001 PHE N 92 TYR 0.021 0.001 TYR M 87 ARG 0.008 0.000 ARG A 646 Details of bonding type rmsd hydrogen bonds : bond 0.05318 ( 114) hydrogen bonds : angle 6.91312 ( 318) SS BOND : bond 0.00470 ( 2) SS BOND : angle 0.46142 ( 4) covalent geometry : bond 0.00285 ( 7938) covalent geometry : angle 0.71618 (10770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.870 Fit side-chains REVERT: H 6 GLU cc_start: 0.7989 (mp0) cc_final: 0.7373 (mp0) REVERT: H 12 VAL cc_start: 0.7917 (OUTLIER) cc_final: 0.7700 (t) REVERT: H 79 LYS cc_start: 0.9243 (mmtp) cc_final: 0.8916 (mmtm) REVERT: H 101 MET cc_start: 0.8727 (mmm) cc_final: 0.8458 (mtm) REVERT: L 35 TRP cc_start: 0.7166 (m-10) cc_final: 0.6832 (m-10) REVERT: L 37 GLN cc_start: 0.9442 (tm-30) cc_final: 0.8876 (tm-30) REVERT: L 38 GLN cc_start: 0.9067 (pp30) cc_final: 0.8593 (pm20) REVERT: L 42 GLN cc_start: 0.8505 (mp10) cc_final: 0.8262 (mp10) REVERT: L 55 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7886 (tm-30) REVERT: L 78 LEU cc_start: 0.8938 (mm) cc_final: 0.8546 (mt) REVERT: L 79 GLU cc_start: 0.8789 (tp30) cc_final: 0.8486 (tp30) REVERT: L 101 ASN cc_start: 0.8896 (p0) cc_final: 0.8570 (p0) REVERT: A 125 PHE cc_start: 0.8502 (m-10) cc_final: 0.7962 (m-10) REVERT: A 147 MET cc_start: 0.8048 (tmm) cc_final: 0.7765 (tmm) REVERT: A 313 LYS cc_start: 0.9318 (tppp) cc_final: 0.9081 (tppt) REVERT: A 352 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.7397 (t70) REVERT: A 486 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8472 (tm-30) REVERT: A 492 MET cc_start: 0.9297 (tmm) cc_final: 0.8963 (tmm) REVERT: A 569 GLU cc_start: 0.8764 (pm20) cc_final: 0.8476 (pm20) REVERT: A 589 GLN cc_start: 0.8493 (pm20) cc_final: 0.8203 (pm20) REVERT: A 593 GLN cc_start: 0.9081 (pm20) cc_final: 0.8594 (pm20) REVERT: A 609 HIS cc_start: 0.8147 (m90) cc_final: 0.7668 (m90) REVERT: A 635 ASN cc_start: 0.9027 (p0) cc_final: 0.8698 (m-40) REVERT: A 663 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8443 (tm-30) REVERT: M 2 LEU cc_start: 0.8673 (pt) cc_final: 0.8452 (pp) REVERT: M 36 TYR cc_start: 0.6912 (m-80) cc_final: 0.6008 (m-80) REVERT: M 61 ARG cc_start: 0.7534 (ptt180) cc_final: 0.7291 (ptt180) REVERT: M 92 PHE cc_start: 0.4305 (OUTLIER) cc_final: 0.3610 (t80) REVERT: N 34 MET cc_start: 0.9175 (mmp) cc_final: 0.8612 (mmp) REVERT: N 36 TRP cc_start: 0.8071 (m100) cc_final: 0.7576 (m100) REVERT: N 50 THR cc_start: 0.9112 (t) cc_final: 0.8180 (p) REVERT: N 62 TRP cc_start: 0.8455 (m100) cc_final: 0.8129 (m100) outliers start: 33 outliers final: 17 residues processed: 219 average time/residue: 0.1988 time to fit residues: 58.1202 Evaluate side-chains 205 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 77 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 30 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN H 100 ASN A 299 HIS M 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.147639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107674 restraints weight = 15783.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107491 restraints weight = 7601.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108252 restraints weight = 6463.109| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7940 Z= 0.213 Angle : 0.744 9.351 10774 Z= 0.389 Chirality : 0.046 0.172 1220 Planarity : 0.005 0.053 1374 Dihedral : 7.122 54.622 1105 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.26 % Favored : 85.74 % Rotamer: Outliers : 5.47 % Allowed : 21.54 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.10 (0.24), residues: 989 helix: -2.20 (0.52), residues: 76 sheet: -2.37 (0.31), residues: 272 loop : -3.12 (0.21), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 300 HIS 0.005 0.001 HIS A 610 PHE 0.024 0.002 PHE A 219 TYR 0.017 0.002 TYR M 87 ARG 0.003 0.000 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.05516 ( 114) hydrogen bonds : angle 6.77397 ( 318) SS BOND : bond 0.00823 ( 2) SS BOND : angle 1.54935 ( 4) covalent geometry : bond 0.00474 ( 7938) covalent geometry : angle 0.74337 (10770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.8090 (mp0) cc_final: 0.7637 (mp0) REVERT: H 34 MET cc_start: 0.8642 (mmm) cc_final: 0.8268 (mmm) REVERT: H 46 GLU cc_start: 0.6794 (tt0) cc_final: 0.6570 (tt0) REVERT: H 79 LYS cc_start: 0.9264 (mmtp) cc_final: 0.8922 (mmtm) REVERT: L 37 GLN cc_start: 0.9455 (tm-30) cc_final: 0.8933 (tm-30) REVERT: L 38 GLN cc_start: 0.9048 (pp30) cc_final: 0.8543 (pm20) REVERT: L 39 LYS cc_start: 0.9005 (tppt) cc_final: 0.8488 (tppt) REVERT: L 42 GLN cc_start: 0.8483 (mp10) cc_final: 0.8147 (mp10) REVERT: L 78 LEU cc_start: 0.8908 (mm) cc_final: 0.8683 (mm) REVERT: L 79 GLU cc_start: 0.8831 (tp30) cc_final: 0.8617 (tp30) REVERT: L 101 ASN cc_start: 0.8728 (p0) cc_final: 0.8494 (p0) REVERT: A 83 MET cc_start: 0.8164 (tpp) cc_final: 0.7808 (mmm) REVERT: A 125 PHE cc_start: 0.8375 (m-10) cc_final: 0.7908 (m-10) REVERT: A 147 MET cc_start: 0.8208 (tmm) cc_final: 0.7353 (tmm) REVERT: A 181 TYR cc_start: 0.7569 (m-80) cc_final: 0.7215 (m-10) REVERT: A 313 LYS cc_start: 0.9311 (tppp) cc_final: 0.9096 (tppt) REVERT: A 486 GLU cc_start: 0.8976 (tm-30) cc_final: 0.7964 (tm-30) REVERT: A 492 MET cc_start: 0.9253 (tmm) cc_final: 0.8966 (tmm) REVERT: A 609 HIS cc_start: 0.8108 (m90) cc_final: 0.7688 (m90) REVERT: A 635 ASN cc_start: 0.8984 (p0) cc_final: 0.8736 (m-40) REVERT: A 644 TYR cc_start: 0.8787 (m-10) cc_final: 0.8558 (m-80) REVERT: A 647 ASP cc_start: 0.8822 (t0) cc_final: 0.8615 (t0) REVERT: A 663 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8364 (tm-30) REVERT: M 36 TYR cc_start: 0.7024 (m-80) cc_final: 0.6108 (m-80) REVERT: M 61 ARG cc_start: 0.7681 (ptt180) cc_final: 0.7477 (ptt180) REVERT: M 92 PHE cc_start: 0.4326 (OUTLIER) cc_final: 0.3541 (t80) REVERT: N 34 MET cc_start: 0.9237 (mmp) cc_final: 0.8622 (mmp) REVERT: N 36 TRP cc_start: 0.8015 (m100) cc_final: 0.7679 (m100) REVERT: N 50 THR cc_start: 0.9030 (t) cc_final: 0.7853 (p) REVERT: N 62 TRP cc_start: 0.8372 (m100) cc_final: 0.7930 (m100) REVERT: N 71 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.6985 (ttm170) outliers start: 47 outliers final: 33 residues processed: 206 average time/residue: 0.1997 time to fit residues: 55.4106 Evaluate side-chains 212 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 27 PHE Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 9.9990 chunk 95 optimal weight: 50.0000 chunk 88 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN H 100 ASN A 77 HIS A 669 GLN M 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.144742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104994 restraints weight = 15932.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104834 restraints weight = 7826.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.105523 restraints weight = 6657.875| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7940 Z= 0.263 Angle : 0.775 8.992 10774 Z= 0.407 Chirality : 0.047 0.173 1220 Planarity : 0.005 0.053 1374 Dihedral : 7.332 54.983 1105 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.47 % Favored : 84.53 % Rotamer: Outliers : 6.05 % Allowed : 21.77 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.03 (0.24), residues: 989 helix: -1.97 (0.52), residues: 76 sheet: -2.35 (0.32), residues: 268 loop : -3.09 (0.21), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 300 HIS 0.005 0.001 HIS A 610 PHE 0.024 0.002 PHE A 219 TYR 0.016 0.002 TYR M 87 ARG 0.003 0.001 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.05413 ( 114) hydrogen bonds : angle 6.80476 ( 318) SS BOND : bond 0.00881 ( 2) SS BOND : angle 1.99291 ( 4) covalent geometry : bond 0.00588 ( 7938) covalent geometry : angle 0.77455 (10770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: H 6 GLU cc_start: 0.8041 (mp0) cc_final: 0.7563 (mp0) REVERT: H 34 MET cc_start: 0.8760 (mmm) cc_final: 0.8405 (mmm) REVERT: H 46 GLU cc_start: 0.6848 (tt0) cc_final: 0.6536 (tt0) REVERT: H 79 LYS cc_start: 0.9270 (mmtp) cc_final: 0.8936 (mmtm) REVERT: L 35 TRP cc_start: 0.7781 (OUTLIER) cc_final: 0.6782 (m-10) REVERT: L 37 GLN cc_start: 0.9435 (tm-30) cc_final: 0.9158 (tm-30) REVERT: L 38 GLN cc_start: 0.9088 (pp30) cc_final: 0.8476 (pm20) REVERT: L 42 GLN cc_start: 0.8498 (mp10) cc_final: 0.8295 (mp10) REVERT: L 78 LEU cc_start: 0.8912 (mm) cc_final: 0.8700 (mm) REVERT: A 83 MET cc_start: 0.8223 (tpp) cc_final: 0.7971 (mmm) REVERT: A 125 PHE cc_start: 0.8428 (m-10) cc_final: 0.8035 (m-10) REVERT: A 147 MET cc_start: 0.8026 (tmm) cc_final: 0.7097 (tmm) REVERT: A 313 LYS cc_start: 0.9349 (tppp) cc_final: 0.9098 (tppt) REVERT: A 486 GLU cc_start: 0.8961 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 492 MET cc_start: 0.9256 (tmm) cc_final: 0.8982 (tmm) REVERT: A 609 HIS cc_start: 0.8137 (m90) cc_final: 0.7766 (m90) REVERT: A 644 TYR cc_start: 0.8852 (m-10) cc_final: 0.8605 (m-80) REVERT: A 663 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8418 (tm-30) REVERT: M 36 TYR cc_start: 0.7029 (m-80) cc_final: 0.6166 (m-80) REVERT: M 61 ARG cc_start: 0.7715 (ptt180) cc_final: 0.7503 (ptt180) REVERT: M 92 PHE cc_start: 0.4512 (OUTLIER) cc_final: 0.3680 (t80) REVERT: N 34 MET cc_start: 0.9235 (mmp) cc_final: 0.8993 (mmp) REVERT: N 36 TRP cc_start: 0.8149 (m100) cc_final: 0.7777 (m100) REVERT: N 71 ARG cc_start: 0.7726 (ttm-80) cc_final: 0.7011 (ttm170) REVERT: N 108 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8195 (m-40) outliers start: 52 outliers final: 41 residues processed: 210 average time/residue: 0.1825 time to fit residues: 52.1844 Evaluate side-chains 221 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain M residue 106 LYS Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 108 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 64 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN H 100 ASN M 6 GLN M 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.146463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106434 restraints weight = 15762.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.106389 restraints weight = 7734.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.107035 restraints weight = 6544.751| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7940 Z= 0.214 Angle : 0.750 9.058 10774 Z= 0.390 Chirality : 0.046 0.168 1220 Planarity : 0.005 0.055 1374 Dihedral : 7.148 54.026 1105 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.07 % Favored : 84.93 % Rotamer: Outliers : 6.75 % Allowed : 23.17 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.89 (0.24), residues: 989 helix: -1.67 (0.53), residues: 76 sheet: -2.27 (0.32), residues: 261 loop : -3.02 (0.21), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 300 HIS 0.004 0.001 HIS A 316 PHE 0.017 0.002 PHE A 219 TYR 0.019 0.002 TYR M 87 ARG 0.003 0.000 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.04919 ( 114) hydrogen bonds : angle 6.58096 ( 318) SS BOND : bond 0.01870 ( 2) SS BOND : angle 4.92189 ( 4) covalent geometry : bond 0.00480 ( 7938) covalent geometry : angle 0.74379 (10770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 186 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: H 6 GLU cc_start: 0.8059 (mp0) cc_final: 0.7613 (mp0) REVERT: H 34 MET cc_start: 0.8760 (mmm) cc_final: 0.8411 (mmm) REVERT: H 46 GLU cc_start: 0.6781 (tt0) cc_final: 0.6488 (tt0) REVERT: H 66 ARG cc_start: 0.9321 (mmm-85) cc_final: 0.8989 (mmm-85) REVERT: H 79 LYS cc_start: 0.9289 (mmtp) cc_final: 0.8964 (mmtm) REVERT: L 35 TRP cc_start: 0.7776 (OUTLIER) cc_final: 0.6783 (m-10) REVERT: L 37 GLN cc_start: 0.9444 (tm-30) cc_final: 0.9178 (tm-30) REVERT: L 38 GLN cc_start: 0.9078 (pp30) cc_final: 0.8481 (pm20) REVERT: L 70 GLU cc_start: 0.8794 (pp20) cc_final: 0.8414 (pp20) REVERT: L 78 LEU cc_start: 0.8909 (mm) cc_final: 0.8691 (mm) REVERT: A 83 MET cc_start: 0.8111 (tpp) cc_final: 0.7889 (mmm) REVERT: A 125 PHE cc_start: 0.8416 (m-10) cc_final: 0.8015 (m-10) REVERT: A 147 MET cc_start: 0.8073 (tmm) cc_final: 0.7162 (tmm) REVERT: A 181 TYR cc_start: 0.7475 (m-80) cc_final: 0.7198 (m-80) REVERT: A 313 LYS cc_start: 0.9359 (tppp) cc_final: 0.9114 (tppt) REVERT: A 486 GLU cc_start: 0.8942 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 492 MET cc_start: 0.9233 (tmm) cc_final: 0.8975 (tmm) REVERT: A 609 HIS cc_start: 0.8113 (m90) cc_final: 0.7734 (m90) REVERT: A 644 TYR cc_start: 0.8818 (m-10) cc_final: 0.8600 (m-80) REVERT: A 653 ASN cc_start: 0.8949 (t0) cc_final: 0.8378 (t0) REVERT: A 663 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8390 (tm-30) REVERT: M 36 TYR cc_start: 0.6963 (m-80) cc_final: 0.6145 (m-80) REVERT: M 61 ARG cc_start: 0.7732 (ptt180) cc_final: 0.7525 (ptt180) REVERT: M 69 THR cc_start: 0.6159 (OUTLIER) cc_final: 0.5931 (m) REVERT: M 92 PHE cc_start: 0.4244 (OUTLIER) cc_final: 0.3463 (t80) REVERT: M 99 ASN cc_start: 0.8820 (t0) cc_final: 0.8453 (t0) REVERT: N 34 MET cc_start: 0.9224 (mmp) cc_final: 0.8627 (mmp) REVERT: N 36 TRP cc_start: 0.8052 (m100) cc_final: 0.7784 (m100) REVERT: N 50 THR cc_start: 0.9000 (t) cc_final: 0.7824 (p) REVERT: N 62 TRP cc_start: 0.8158 (m100) cc_final: 0.7795 (m100) REVERT: N 71 ARG cc_start: 0.7748 (ttm-80) cc_final: 0.7097 (ttm170) REVERT: N 108 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8115 (m-40) outliers start: 58 outliers final: 43 residues processed: 219 average time/residue: 0.1808 time to fit residues: 54.6089 Evaluate side-chains 223 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain M residue 106 LYS Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 108 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 13 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 10 optimal weight: 0.0000 chunk 75 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN H 100 ASN A 264 ASN A 669 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.148122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100963 restraints weight = 15779.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104028 restraints weight = 8793.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106135 restraints weight = 6036.596| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7940 Z= 0.155 Angle : 0.720 8.543 10774 Z= 0.372 Chirality : 0.045 0.152 1220 Planarity : 0.004 0.052 1374 Dihedral : 6.801 51.911 1105 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.65 % Favored : 86.35 % Rotamer: Outliers : 6.40 % Allowed : 24.80 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.76 (0.24), residues: 989 helix: -1.34 (0.56), residues: 76 sheet: -2.27 (0.32), residues: 266 loop : -2.90 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 35 HIS 0.003 0.000 HIS A 316 PHE 0.012 0.001 PHE A 219 TYR 0.015 0.001 TYR M 87 ARG 0.002 0.000 ARG H 95 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 114) hydrogen bonds : angle 6.19903 ( 318) SS BOND : bond 0.01236 ( 2) SS BOND : angle 3.30498 ( 4) covalent geometry : bond 0.00346 ( 7938) covalent geometry : angle 0.71759 (10770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: H 6 GLU cc_start: 0.7932 (mp0) cc_final: 0.7538 (mp0) REVERT: H 32 TYR cc_start: 0.9019 (m-10) cc_final: 0.8798 (m-80) REVERT: H 34 MET cc_start: 0.8810 (mmm) cc_final: 0.8334 (mmm) REVERT: H 79 LYS cc_start: 0.9248 (mmtp) cc_final: 0.8916 (mmtm) REVERT: L 35 TRP cc_start: 0.7609 (OUTLIER) cc_final: 0.6710 (m-10) REVERT: L 37 GLN cc_start: 0.9409 (tm-30) cc_final: 0.8961 (tm-30) REVERT: L 38 GLN cc_start: 0.8995 (pp30) cc_final: 0.8487 (pm20) REVERT: L 70 GLU cc_start: 0.8791 (pp20) cc_final: 0.8385 (pp20) REVERT: A 125 PHE cc_start: 0.8439 (m-10) cc_final: 0.8065 (m-10) REVERT: A 147 MET cc_start: 0.7931 (tmm) cc_final: 0.7007 (tmm) REVERT: A 181 TYR cc_start: 0.7415 (m-80) cc_final: 0.7098 (m-10) REVERT: A 313 LYS cc_start: 0.9327 (tppp) cc_final: 0.9082 (tppt) REVERT: A 486 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8328 (tm-30) REVERT: A 492 MET cc_start: 0.9273 (tmm) cc_final: 0.8961 (tmm) REVERT: A 600 ASN cc_start: 0.8816 (t0) cc_final: 0.8605 (t0) REVERT: A 609 HIS cc_start: 0.8099 (m90) cc_final: 0.7714 (m90) REVERT: A 644 TYR cc_start: 0.8797 (m-10) cc_final: 0.8583 (m-80) REVERT: A 663 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8429 (tm-30) REVERT: M 36 TYR cc_start: 0.6932 (m-80) cc_final: 0.6093 (m-80) REVERT: M 42 GLN cc_start: 0.7823 (tp-100) cc_final: 0.7549 (tp-100) REVERT: M 69 THR cc_start: 0.6076 (OUTLIER) cc_final: 0.5854 (m) REVERT: M 92 PHE cc_start: 0.4110 (OUTLIER) cc_final: 0.3465 (t80) REVERT: M 99 ASN cc_start: 0.8918 (t0) cc_final: 0.8527 (t0) REVERT: N 34 MET cc_start: 0.9107 (mmp) cc_final: 0.8467 (mmp) REVERT: N 36 TRP cc_start: 0.7839 (m100) cc_final: 0.7563 (m100) REVERT: N 50 THR cc_start: 0.9004 (t) cc_final: 0.7830 (p) REVERT: N 71 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7088 (ttm170) REVERT: N 108 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8049 (m-40) outliers start: 55 outliers final: 39 residues processed: 220 average time/residue: 0.1787 time to fit residues: 53.6208 Evaluate side-chains 226 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain M residue 106 LYS Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 108 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 40 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 0.0870 chunk 8 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 92 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 overall best weight: 1.3740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN H 100 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.149567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.103430 restraints weight = 16261.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106286 restraints weight = 8506.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.108062 restraints weight = 5137.505| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7940 Z= 0.123 Angle : 0.696 9.288 10774 Z= 0.355 Chirality : 0.044 0.144 1220 Planarity : 0.004 0.048 1374 Dihedral : 6.289 49.024 1105 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 5.94 % Allowed : 24.91 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.57 (0.25), residues: 989 helix: -1.01 (0.56), residues: 76 sheet: -2.08 (0.32), residues: 265 loop : -2.83 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 35 HIS 0.002 0.000 HIS A 316 PHE 0.008 0.001 PHE A 219 TYR 0.013 0.001 TYR M 87 ARG 0.003 0.000 ARG H 95 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 114) hydrogen bonds : angle 5.90986 ( 318) SS BOND : bond 0.01242 ( 2) SS BOND : angle 2.74327 ( 4) covalent geometry : bond 0.00273 ( 7938) covalent geometry : angle 0.69431 (10770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.9006 (mmm) cc_final: 0.8771 (mmm) REVERT: H 46 GLU cc_start: 0.6380 (tt0) cc_final: 0.5855 (tt0) REVERT: H 79 LYS cc_start: 0.9173 (mmtp) cc_final: 0.8857 (mmtm) REVERT: L 35 TRP cc_start: 0.7369 (OUTLIER) cc_final: 0.6543 (m-10) REVERT: L 37 GLN cc_start: 0.9363 (tm-30) cc_final: 0.8932 (tm-30) REVERT: L 38 GLN cc_start: 0.8925 (pp30) cc_final: 0.8343 (pm20) REVERT: L 39 LYS cc_start: 0.8909 (tppt) cc_final: 0.8620 (tppt) REVERT: L 70 GLU cc_start: 0.8768 (pp20) cc_final: 0.8337 (pp20) REVERT: A 83 MET cc_start: 0.8626 (mmm) cc_final: 0.8208 (mmm) REVERT: A 147 MET cc_start: 0.7663 (tmm) cc_final: 0.7267 (tmm) REVERT: A 181 TYR cc_start: 0.7338 (m-80) cc_final: 0.7006 (m-10) REVERT: A 231 GLU cc_start: 0.8622 (mp0) cc_final: 0.8386 (mp0) REVERT: A 313 LYS cc_start: 0.9332 (tppp) cc_final: 0.9033 (tppt) REVERT: A 486 GLU cc_start: 0.8875 (tm-30) cc_final: 0.7953 (tm-30) REVERT: A 492 MET cc_start: 0.9319 (tmm) cc_final: 0.8984 (tmm) REVERT: A 569 GLU cc_start: 0.8894 (pm20) cc_final: 0.8613 (pm20) REVERT: A 609 HIS cc_start: 0.8050 (m90) cc_final: 0.7654 (m90) REVERT: A 644 TYR cc_start: 0.8757 (m-10) cc_final: 0.8543 (m-80) REVERT: A 653 ASN cc_start: 0.8970 (t0) cc_final: 0.8378 (t0) REVERT: A 663 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8410 (tm-30) REVERT: M 36 TYR cc_start: 0.6993 (m-80) cc_final: 0.6248 (m-80) REVERT: M 69 THR cc_start: 0.5858 (OUTLIER) cc_final: 0.5608 (m) REVERT: M 92 PHE cc_start: 0.3939 (OUTLIER) cc_final: 0.3699 (t80) REVERT: M 99 ASN cc_start: 0.8949 (t0) cc_final: 0.8701 (t0) REVERT: N 34 MET cc_start: 0.8934 (mmp) cc_final: 0.8256 (mmp) REVERT: N 36 TRP cc_start: 0.7580 (m100) cc_final: 0.7241 (m100) REVERT: N 50 THR cc_start: 0.8990 (t) cc_final: 0.7891 (p) REVERT: N 62 TRP cc_start: 0.8207 (m100) cc_final: 0.7975 (m100) REVERT: N 71 ARG cc_start: 0.7655 (ttm-80) cc_final: 0.7021 (ttm170) REVERT: N 108 ASN cc_start: 0.8075 (OUTLIER) cc_final: 0.7690 (m-40) outliers start: 51 outliers final: 35 residues processed: 218 average time/residue: 0.1858 time to fit residues: 55.2235 Evaluate side-chains 221 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain M residue 106 LYS Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 108 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 68 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 49 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN H 100 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.149795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100912 restraints weight = 16652.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.104532 restraints weight = 8395.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106928 restraints weight = 5526.984| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7940 Z= 0.125 Angle : 0.715 9.989 10774 Z= 0.363 Chirality : 0.044 0.163 1220 Planarity : 0.004 0.048 1374 Dihedral : 6.131 48.543 1105 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer: Outliers : 5.36 % Allowed : 25.96 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.47 (0.25), residues: 989 helix: -0.75 (0.57), residues: 76 sheet: -2.01 (0.32), residues: 260 loop : -2.79 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 35 HIS 0.002 0.000 HIS A 316 PHE 0.009 0.001 PHE A 219 TYR 0.017 0.001 TYR H 32 ARG 0.003 0.000 ARG H 95 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 114) hydrogen bonds : angle 5.79727 ( 318) SS BOND : bond 0.00943 ( 2) SS BOND : angle 2.48219 ( 4) covalent geometry : bond 0.00276 ( 7938) covalent geometry : angle 0.71309 (10770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8983 (mmm) cc_final: 0.8750 (mmm) REVERT: H 46 GLU cc_start: 0.6394 (tt0) cc_final: 0.5857 (tt0) REVERT: H 93 CYS cc_start: 0.8148 (m) cc_final: 0.7856 (t) REVERT: L 35 TRP cc_start: 0.7381 (OUTLIER) cc_final: 0.6543 (m-10) REVERT: L 37 GLN cc_start: 0.9382 (tm-30) cc_final: 0.8913 (tm-30) REVERT: L 38 GLN cc_start: 0.8907 (pp30) cc_final: 0.8480 (pm20) REVERT: L 70 GLU cc_start: 0.8758 (pp20) cc_final: 0.8334 (pp20) REVERT: A 147 MET cc_start: 0.7711 (tmm) cc_final: 0.7317 (tmm) REVERT: A 181 TYR cc_start: 0.7192 (m-80) cc_final: 0.6895 (m-10) REVERT: A 313 LYS cc_start: 0.9342 (tppp) cc_final: 0.9041 (tppt) REVERT: A 486 GLU cc_start: 0.8868 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 492 MET cc_start: 0.9315 (tmm) cc_final: 0.9026 (tmm) REVERT: A 569 GLU cc_start: 0.8900 (pm20) cc_final: 0.8629 (pm20) REVERT: A 609 HIS cc_start: 0.8082 (m90) cc_final: 0.7687 (m90) REVERT: A 644 TYR cc_start: 0.8757 (m-10) cc_final: 0.8533 (m-80) REVERT: A 653 ASN cc_start: 0.8985 (t0) cc_final: 0.8457 (t0) REVERT: A 663 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8470 (tm-30) REVERT: M 36 TYR cc_start: 0.6873 (m-80) cc_final: 0.6137 (m-80) REVERT: M 42 GLN cc_start: 0.7787 (tp-100) cc_final: 0.7561 (tp-100) REVERT: M 69 THR cc_start: 0.5904 (OUTLIER) cc_final: 0.5645 (m) REVERT: M 77 ASP cc_start: 0.8645 (m-30) cc_final: 0.8317 (m-30) REVERT: M 92 PHE cc_start: 0.3980 (OUTLIER) cc_final: 0.3721 (t80) REVERT: M 99 ASN cc_start: 0.8995 (t0) cc_final: 0.8771 (t0) REVERT: N 32 TYR cc_start: 0.7882 (m-80) cc_final: 0.7641 (m-10) REVERT: N 34 MET cc_start: 0.8956 (mmp) cc_final: 0.8704 (mmp) REVERT: N 36 TRP cc_start: 0.7491 (m100) cc_final: 0.7191 (m100) REVERT: N 71 ARG cc_start: 0.7620 (ttm-80) cc_final: 0.7046 (ttm170) REVERT: N 108 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7792 (m-40) outliers start: 46 outliers final: 37 residues processed: 215 average time/residue: 0.1844 time to fit residues: 54.2809 Evaluate side-chains 231 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain M residue 106 LYS Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 59 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 108 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 11 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 25 optimal weight: 0.0000 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN H 100 ASN A 600 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.151329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111192 restraints weight = 16864.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110809 restraints weight = 8229.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111407 restraints weight = 7982.314| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7940 Z= 0.121 Angle : 0.722 10.300 10774 Z= 0.363 Chirality : 0.044 0.148 1220 Planarity : 0.004 0.042 1374 Dihedral : 5.894 48.722 1105 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 5.70 % Allowed : 26.31 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.33 (0.25), residues: 989 helix: -0.29 (0.60), residues: 72 sheet: -1.88 (0.33), residues: 251 loop : -2.75 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 35 HIS 0.001 0.000 HIS A 316 PHE 0.010 0.001 PHE N 92 TYR 0.015 0.001 TYR M 87 ARG 0.007 0.000 ARG M 61 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 114) hydrogen bonds : angle 5.59151 ( 318) SS BOND : bond 0.00512 ( 2) SS BOND : angle 1.72709 ( 4) covalent geometry : bond 0.00268 ( 7938) covalent geometry : angle 0.72110 (10770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8968 (mmm) cc_final: 0.8722 (mmm) REVERT: H 46 GLU cc_start: 0.6466 (tt0) cc_final: 0.5923 (tt0) REVERT: L 35 TRP cc_start: 0.7368 (OUTLIER) cc_final: 0.6653 (m-10) REVERT: L 37 GLN cc_start: 0.9355 (tm-30) cc_final: 0.8860 (tm-30) REVERT: L 39 LYS cc_start: 0.8984 (tppt) cc_final: 0.8448 (tppt) REVERT: L 100 PHE cc_start: 0.9009 (m-80) cc_final: 0.8595 (m-80) REVERT: A 83 MET cc_start: 0.7925 (mmm) cc_final: 0.7544 (mmm) REVERT: A 147 MET cc_start: 0.7779 (tmm) cc_final: 0.7396 (tmm) REVERT: A 181 TYR cc_start: 0.7178 (m-80) cc_final: 0.6919 (m-10) REVERT: A 313 LYS cc_start: 0.9338 (tppp) cc_final: 0.9029 (tppt) REVERT: A 344 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7416 (mp0) REVERT: A 486 GLU cc_start: 0.8860 (tm-30) cc_final: 0.7901 (tm-30) REVERT: A 492 MET cc_start: 0.9328 (tmm) cc_final: 0.9021 (tmm) REVERT: A 501 ASN cc_start: 0.8837 (p0) cc_final: 0.8095 (p0) REVERT: A 569 GLU cc_start: 0.8914 (pm20) cc_final: 0.8682 (pm20) REVERT: A 609 HIS cc_start: 0.8105 (m90) cc_final: 0.7700 (m90) REVERT: A 644 TYR cc_start: 0.8751 (m-10) cc_final: 0.8531 (m-80) REVERT: A 653 ASN cc_start: 0.8996 (t0) cc_final: 0.8515 (t0) REVERT: A 663 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8668 (tm-30) REVERT: M 36 TYR cc_start: 0.6867 (m-80) cc_final: 0.6153 (m-80) REVERT: M 42 GLN cc_start: 0.8003 (tp-100) cc_final: 0.7746 (tp-100) REVERT: M 69 THR cc_start: 0.5959 (OUTLIER) cc_final: 0.5708 (m) REVERT: M 92 PHE cc_start: 0.3840 (OUTLIER) cc_final: 0.3631 (t80) REVERT: M 99 ASN cc_start: 0.9034 (t0) cc_final: 0.8801 (t0) REVERT: N 34 MET cc_start: 0.8880 (mmp) cc_final: 0.8660 (mmp) REVERT: N 36 TRP cc_start: 0.7423 (m100) cc_final: 0.7178 (m100) REVERT: N 71 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7110 (ttm170) REVERT: N 108 ASN cc_start: 0.7879 (OUTLIER) cc_final: 0.7399 (m-40) outliers start: 49 outliers final: 40 residues processed: 224 average time/residue: 0.1847 time to fit residues: 56.3477 Evaluate side-chains 241 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain M residue 106 LYS Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 59 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 108 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 46 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN H 100 ASN A 359 GLN A 533 GLN A 600 ASN A 669 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.147388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097890 restraints weight = 16859.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.101388 restraints weight = 8715.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.103703 restraints weight = 5787.406| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7940 Z= 0.200 Angle : 0.757 9.018 10774 Z= 0.387 Chirality : 0.045 0.155 1220 Planarity : 0.004 0.041 1374 Dihedral : 6.302 50.710 1105 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 5.01 % Allowed : 26.89 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.47 (0.25), residues: 989 helix: -0.71 (0.60), residues: 70 sheet: -2.03 (0.32), residues: 265 loop : -2.77 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP N 62 HIS 0.004 0.001 HIS A 610 PHE 0.015 0.001 PHE A 219 TYR 0.016 0.002 TYR M 87 ARG 0.003 0.000 ARG N 95 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 114) hydrogen bonds : angle 5.87625 ( 318) SS BOND : bond 0.00464 ( 2) SS BOND : angle 2.02745 ( 4) covalent geometry : bond 0.00448 ( 7938) covalent geometry : angle 0.75601 (10770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8896 (mmm) cc_final: 0.8359 (mmm) REVERT: H 46 GLU cc_start: 0.6439 (tt0) cc_final: 0.5887 (tt0) REVERT: L 35 TRP cc_start: 0.7490 (OUTLIER) cc_final: 0.6419 (m-10) REVERT: L 37 GLN cc_start: 0.9356 (tm-30) cc_final: 0.8834 (tm-30) REVERT: L 70 GLU cc_start: 0.8758 (pp20) cc_final: 0.8385 (pp20) REVERT: L 79 GLU cc_start: 0.8515 (tp30) cc_final: 0.8136 (tp30) REVERT: L 100 PHE cc_start: 0.8973 (m-80) cc_final: 0.8584 (m-80) REVERT: A 83 MET cc_start: 0.8770 (mmm) cc_final: 0.8376 (mmm) REVERT: A 147 MET cc_start: 0.7680 (tmm) cc_final: 0.6742 (tmm) REVERT: A 313 LYS cc_start: 0.9358 (tppp) cc_final: 0.9069 (tppt) REVERT: A 492 MET cc_start: 0.9311 (tmm) cc_final: 0.8996 (tmm) REVERT: A 569 GLU cc_start: 0.8911 (pm20) cc_final: 0.8673 (pm20) REVERT: A 609 HIS cc_start: 0.8121 (m90) cc_final: 0.7730 (m90) REVERT: A 653 ASN cc_start: 0.8998 (t0) cc_final: 0.8541 (t0) REVERT: A 663 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8492 (tm-30) REVERT: M 42 GLN cc_start: 0.8120 (tp-100) cc_final: 0.7863 (tp-100) REVERT: M 69 THR cc_start: 0.5976 (OUTLIER) cc_final: 0.5727 (m) REVERT: M 99 ASN cc_start: 0.9065 (t0) cc_final: 0.8779 (t0) REVERT: N 34 MET cc_start: 0.9062 (mmp) cc_final: 0.8763 (mmp) REVERT: N 36 TRP cc_start: 0.7547 (m100) cc_final: 0.7314 (m100) REVERT: N 71 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.6946 (ttm170) REVERT: N 108 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7664 (m-40) outliers start: 43 outliers final: 35 residues processed: 213 average time/residue: 0.1863 time to fit residues: 54.4104 Evaluate side-chains 228 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain M residue 106 LYS Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 108 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 0.0270 chunk 74 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 overall best weight: 1.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN H 100 ASN A 600 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.150705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103800 restraints weight = 16448.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.106421 restraints weight = 9741.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107999 restraints weight = 5763.262| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7940 Z= 0.127 Angle : 0.738 10.295 10774 Z= 0.372 Chirality : 0.044 0.161 1220 Planarity : 0.004 0.047 1374 Dihedral : 5.885 51.452 1103 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 5.24 % Allowed : 27.12 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.27 (0.25), residues: 989 helix: -0.20 (0.61), residues: 72 sheet: -1.94 (0.32), residues: 260 loop : -2.65 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP M 35 HIS 0.002 0.000 HIS A 316 PHE 0.008 0.001 PHE N 92 TYR 0.016 0.001 TYR M 87 ARG 0.013 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 114) hydrogen bonds : angle 5.58374 ( 318) SS BOND : bond 0.00446 ( 2) SS BOND : angle 1.82092 ( 4) covalent geometry : bond 0.00286 ( 7938) covalent geometry : angle 0.73720 (10770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3079.94 seconds wall clock time: 54 minutes 4.82 seconds (3244.82 seconds total)