Starting phenix.real_space_refine on Tue Sep 24 01:07:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/09_2024/6vrk_21369.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/09_2024/6vrk_21369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/09_2024/6vrk_21369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/09_2024/6vrk_21369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/09_2024/6vrk_21369.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/09_2024/6vrk_21369.cif" } resolution = 4.1 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= -0.001 sd= 0.975 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 34 5.16 5 C 4045 2.51 5 N 958 2.21 5 O 1103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6141 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4311 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 517} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 924 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'LMT': 1, 'NAG': 2, 'RFS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.94, per 1000 atoms: 0.80 Number of scatterers: 6141 At special positions: 0 Unit cell: (97.2, 102.384, 82.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 34 16.00 O 1103 8.00 N 958 7.00 C 4045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 208 " " NAG A 702 " - " ASN A 217 " Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 866.4 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 7 sheets defined 56.3% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 4.271A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 4.976A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 148 through 154 removed outlier: 4.000A pdb=" N TRP A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 159 through 190 removed outlier: 4.016A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 252 through 271 Processing helix chain 'A' and resid 273 through 285 removed outlier: 4.056A pdb=" N LYS A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.724A pdb=" N ILE A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 removed outlier: 3.945A pdb=" N GLY A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 Processing helix chain 'A' and resid 322 through 338 removed outlier: 4.064A pdb=" N TRP A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 356 through 390 removed outlier: 3.653A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.921A pdb=" N VAL A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'A' and resid 419 through 454 removed outlier: 4.170A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.538A pdb=" N VAL A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 495 removed outlier: 4.287A pdb=" N VAL A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 515 Processing helix chain 'A' and resid 517 through 529 Processing helix chain 'A' and resid 534 through 543 Processing helix chain 'A' and resid 543 through 557 Processing helix chain 'A' and resid 571 through 584 Processing helix chain 'A' and resid 587 through 600 removed outlier: 4.044A pdb=" N THR A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR A 592 " --> pdb=" O CYS A 588 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 599 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 600 " --> pdb=" O ARG A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 613 removed outlier: 3.653A pdb=" N ARG A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.978A pdb=" N TYR B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 96 Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 41 removed outlier: 3.646A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 73 through 74 removed outlier: 6.794A pdb=" N TRP C 55 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR C 69 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 53 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 107 " --> pdb=" O TYR C 56 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 58 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 105 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 30 removed outlier: 5.743A pdb=" N GLU B 29 " --> pdb=" O THR B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.627A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER B 118 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 56 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR B 114 " --> pdb=" O VAL B 56 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 855 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: 1.61 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 1822 1.36 - 1.49: 1931 1.49 - 1.63: 2523 1.63 - 1.76: 0 1.76 - 1.89: 50 Bond restraints: 6326 Sorted by residual: bond pdb=" C06 RFS A 704 " pdb=" C07 RFS A 704 " ideal model delta sigma weight residual 1.511 1.602 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C14 RFS A 704 " pdb=" O15 RFS A 704 " ideal model delta sigma weight residual 1.432 1.499 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C16 RFS A 704 " pdb=" O15 RFS A 704 " ideal model delta sigma weight residual 1.362 1.426 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C07 RFS A 704 " pdb=" C08 RFS A 704 " ideal model delta sigma weight residual 1.394 1.456 -0.062 2.00e-02 2.50e+03 9.53e+00 bond pdb=" C19 RFS A 704 " pdb=" C20 RFS A 704 " ideal model delta sigma weight residual 1.376 1.437 -0.061 2.00e-02 2.50e+03 9.17e+00 ... (remaining 6321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 8493 2.32 - 4.64: 98 4.64 - 6.97: 18 6.97 - 9.29: 9 9.29 - 11.61: 1 Bond angle restraints: 8619 Sorted by residual: angle pdb=" C VAL B 120 " pdb=" N ARG B 121 " pdb=" CA ARG B 121 " ideal model delta sigma weight residual 121.80 133.41 -11.61 2.44e+00 1.68e-01 2.26e+01 angle pdb=" N ILE A 587 " pdb=" CA ILE A 587 " pdb=" C ILE A 587 " ideal model delta sigma weight residual 112.98 107.67 5.31 1.25e+00 6.40e-01 1.81e+01 angle pdb=" N ARG B 121 " pdb=" CA ARG B 121 " pdb=" C ARG B 121 " ideal model delta sigma weight residual 109.81 117.87 -8.06 2.21e+00 2.05e-01 1.33e+01 angle pdb=" C2 LMT A 703 " pdb=" C3 LMT A 703 " pdb=" C4 LMT A 703 " ideal model delta sigma weight residual 117.09 107.89 9.20 3.00e+00 1.11e-01 9.40e+00 angle pdb=" C TRP A 458 " pdb=" N ALA A 459 " pdb=" CA ALA A 459 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.78e+00 ... (remaining 8614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 3320 17.44 - 34.87: 300 34.87 - 52.31: 51 52.31 - 69.75: 12 69.75 - 87.18: 9 Dihedral angle restraints: 3692 sinusoidal: 1478 harmonic: 2214 Sorted by residual: dihedral pdb=" CA ARG B 121 " pdb=" C ARG B 121 " pdb=" N PRO B 122 " pdb=" CA PRO B 122 " ideal model delta harmonic sigma weight residual 180.00 135.50 44.50 0 5.00e+00 4.00e-02 7.92e+01 dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 108 " pdb=" CB CYS C 108 " ideal model delta sinusoidal sigma weight residual -86.00 -33.27 -52.73 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CA TYR B 123 " pdb=" C TYR B 123 " pdb=" N TYR B 124 " pdb=" CA TYR B 124 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 3689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 724 0.042 - 0.083: 196 0.083 - 0.125: 40 0.125 - 0.167: 2 0.167 - 0.208: 4 Chirality restraints: 966 Sorted by residual: chirality pdb=" C5' LMT A 703 " pdb=" C4' LMT A 703 " pdb=" C6' LMT A 703 " pdb=" O5' LMT A 703 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3B LMT A 703 " pdb=" C2B LMT A 703 " pdb=" C4B LMT A 703 " pdb=" O3B LMT A 703 " both_signs ideal model delta sigma weight residual False 2.50 2.29 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C4' LMT A 703 " pdb=" C3' LMT A 703 " pdb=" C5' LMT A 703 " pdb=" O1B LMT A 703 " both_signs ideal model delta sigma weight residual False -2.55 -2.76 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 963 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 121 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO B 122 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 548 " 0.012 2.00e-02 2.50e+03 9.45e-03 1.56e+00 pdb=" CG PHE A 548 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 548 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 548 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 548 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 548 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 548 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 130 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO A 131 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.017 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1363 2.78 - 3.31: 6145 3.31 - 3.84: 10436 3.84 - 4.37: 11804 4.37 - 4.90: 20067 Nonbonded interactions: 49815 Sorted by model distance: nonbonded pdb=" O ARG A 596 " pdb=" OG1 THR A 600 " model vdw 2.245 3.040 nonbonded pdb=" OG1 THR C 51 " pdb=" O SER C 70 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 385 " pdb=" OD1 ASN A 416 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR C 83 " pdb=" O THR C 94 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR A 210 " pdb=" OG SER A 224 " model vdw 2.268 3.040 ... (remaining 49810 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.440 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 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 : 0.004 0.091 6326 Z= 0.246 Angle : 0.686 11.612 8619 Z= 0.350 Chirality : 0.040 0.208 966 Planarity : 0.004 0.065 1048 Dihedral : 13.927 87.184 2277 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.27), residues: 758 helix: -1.01 (0.23), residues: 359 sheet: -3.09 (0.42), residues: 89 loop : -2.93 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 103 HIS 0.005 0.001 HIS C 111 PHE 0.021 0.001 PHE A 548 TYR 0.014 0.001 TYR B 123 ARG 0.002 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7864 (tmtt) cc_final: 0.7388 (tptp) REVERT: A 135 MET cc_start: 0.9118 (tmm) cc_final: 0.8871 (tmm) REVERT: A 152 ARG cc_start: 0.7213 (ttp-110) cc_final: 0.6490 (ttm-80) REVERT: A 229 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8683 (tm-30) REVERT: A 417 MET cc_start: 0.6445 (mtm) cc_final: 0.5830 (mtm) REVERT: A 432 ILE cc_start: 0.8960 (mt) cc_final: 0.8707 (mt) REVERT: A 493 GLU cc_start: 0.6717 (tt0) cc_final: 0.6314 (tt0) REVERT: A 494 GLU cc_start: 0.8033 (tp30) cc_final: 0.7783 (tt0) REVERT: A 563 LEU cc_start: 0.8343 (pt) cc_final: 0.6023 (tt) REVERT: C 48 ASP cc_start: 0.7048 (t0) cc_final: 0.6770 (t0) REVERT: C 99 GLN cc_start: 0.6118 (mt0) cc_final: 0.5802 (mt0) REVERT: B 58 GLN cc_start: 0.6535 (tm-30) cc_final: 0.6331 (tm-30) REVERT: B 109 ASP cc_start: 0.7275 (m-30) cc_final: 0.6728 (m-30) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1755 time to fit residues: 49.4606 Evaluate side-chains 159 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 238 GLN A 240 HIS ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN C 109 GLN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6326 Z= 0.189 Angle : 0.630 13.917 8619 Z= 0.320 Chirality : 0.040 0.160 966 Planarity : 0.004 0.075 1048 Dihedral : 8.294 67.877 961 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.31 % Allowed : 5.54 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.29), residues: 758 helix: -0.11 (0.26), residues: 367 sheet: -2.55 (0.46), residues: 86 loop : -2.58 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 541 HIS 0.002 0.001 HIS A 143 PHE 0.024 0.002 PHE A 548 TYR 0.016 0.001 TYR B 52 ARG 0.006 0.001 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7626 (tmtt) cc_final: 0.7307 (tptp) REVERT: A 107 TYR cc_start: 0.7807 (t80) cc_final: 0.7494 (t80) REVERT: A 180 MET cc_start: 0.8856 (mmp) cc_final: 0.8530 (mmp) REVERT: A 238 GLN cc_start: 0.6385 (tp40) cc_final: 0.6023 (mm-40) REVERT: A 242 SER cc_start: 0.8506 (p) cc_final: 0.8291 (t) REVERT: A 393 ASP cc_start: 0.5002 (t0) cc_final: 0.4800 (t70) REVERT: A 417 MET cc_start: 0.6537 (mtm) cc_final: 0.5943 (mtm) REVERT: A 493 GLU cc_start: 0.6496 (tt0) cc_final: 0.6059 (mt-10) REVERT: A 494 GLU cc_start: 0.8190 (tp30) cc_final: 0.7792 (tt0) REVERT: A 563 LEU cc_start: 0.8504 (pt) cc_final: 0.5826 (tt) REVERT: C 117 THR cc_start: 0.8176 (p) cc_final: 0.7924 (p) REVERT: B 109 ASP cc_start: 0.7344 (m-30) cc_final: 0.7083 (m-30) outliers start: 2 outliers final: 1 residues processed: 183 average time/residue: 0.1522 time to fit residues: 37.4846 Evaluate side-chains 148 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS A 240 HIS ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN C 28 HIS ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6326 Z= 0.200 Angle : 0.651 15.134 8619 Z= 0.328 Chirality : 0.041 0.168 966 Planarity : 0.004 0.070 1048 Dihedral : 8.056 54.260 961 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.30), residues: 758 helix: 0.18 (0.27), residues: 368 sheet: -2.54 (0.47), residues: 97 loop : -2.28 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 541 HIS 0.002 0.001 HIS C 111 PHE 0.023 0.002 PHE A 287 TYR 0.017 0.002 TYR A 121 ARG 0.002 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7613 (tmtt) cc_final: 0.7314 (tptp) REVERT: A 88 PHE cc_start: 0.8312 (t80) cc_final: 0.8063 (t80) REVERT: A 107 TYR cc_start: 0.7890 (t80) cc_final: 0.7606 (t80) REVERT: A 152 ARG cc_start: 0.7150 (ttp-110) cc_final: 0.6125 (ttm-80) REVERT: A 180 MET cc_start: 0.8887 (mmp) cc_final: 0.8512 (mmp) REVERT: A 229 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8610 (tm-30) REVERT: A 242 SER cc_start: 0.8663 (p) cc_final: 0.8362 (t) REVERT: A 306 TRP cc_start: 0.7261 (p-90) cc_final: 0.6206 (m-10) REVERT: A 393 ASP cc_start: 0.5138 (t0) cc_final: 0.4917 (t70) REVERT: A 410 TYR cc_start: 0.8605 (t80) cc_final: 0.7854 (t80) REVERT: A 417 MET cc_start: 0.6599 (mtm) cc_final: 0.6345 (mtm) REVERT: A 493 GLU cc_start: 0.6497 (tt0) cc_final: 0.6192 (tt0) REVERT: A 494 GLU cc_start: 0.8204 (tp30) cc_final: 0.7824 (tt0) REVERT: A 570 TYR cc_start: 0.7895 (m-80) cc_final: 0.7564 (m-80) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1653 time to fit residues: 39.2839 Evaluate side-chains 146 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 68 optimal weight: 0.0040 chunk 72 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 19 optimal weight: 0.4980 chunk 60 optimal weight: 9.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 240 HIS ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6326 Z= 0.175 Angle : 0.642 14.005 8619 Z= 0.322 Chirality : 0.041 0.217 966 Planarity : 0.004 0.070 1048 Dihedral : 7.777 66.158 961 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.30), residues: 758 helix: 0.39 (0.27), residues: 365 sheet: -2.42 (0.46), residues: 101 loop : -2.14 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 458 HIS 0.007 0.001 HIS C 111 PHE 0.037 0.002 PHE A 373 TYR 0.021 0.001 TYR B 114 ARG 0.002 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7575 (tmtt) cc_final: 0.7211 (tptp) REVERT: A 107 TYR cc_start: 0.7918 (t80) cc_final: 0.7687 (t80) REVERT: A 180 MET cc_start: 0.8882 (mmp) cc_final: 0.8380 (mmp) REVERT: A 229 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8577 (tm-30) REVERT: A 242 SER cc_start: 0.8611 (p) cc_final: 0.8348 (t) REVERT: A 313 LEU cc_start: 0.8445 (mm) cc_final: 0.8239 (tp) REVERT: A 314 LYS cc_start: 0.7166 (tttm) cc_final: 0.6641 (mtpt) REVERT: A 393 ASP cc_start: 0.5232 (t0) cc_final: 0.4965 (t70) REVERT: A 410 TYR cc_start: 0.8536 (t80) cc_final: 0.8166 (t80) REVERT: A 437 ASP cc_start: 0.7873 (p0) cc_final: 0.7672 (p0) REVERT: A 493 GLU cc_start: 0.6439 (tt0) cc_final: 0.6219 (tt0) REVERT: A 494 GLU cc_start: 0.8194 (tp30) cc_final: 0.7834 (tt0) REVERT: B 108 GLU cc_start: 0.7703 (pp20) cc_final: 0.7488 (pp20) REVERT: B 133 THR cc_start: 0.7786 (p) cc_final: 0.7511 (p) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1612 time to fit residues: 35.9678 Evaluate side-chains 140 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6326 Z= 0.163 Angle : 0.624 10.323 8619 Z= 0.315 Chirality : 0.040 0.160 966 Planarity : 0.004 0.071 1048 Dihedral : 7.676 74.053 961 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.31), residues: 758 helix: 0.52 (0.27), residues: 369 sheet: -2.31 (0.46), residues: 101 loop : -1.93 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 271 HIS 0.011 0.002 HIS A 143 PHE 0.021 0.001 PHE A 287 TYR 0.015 0.001 TYR B 114 ARG 0.002 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7559 (tmtt) cc_final: 0.7281 (tptp) REVERT: A 107 TYR cc_start: 0.7971 (t80) cc_final: 0.7629 (t80) REVERT: A 180 MET cc_start: 0.8914 (mmp) cc_final: 0.8367 (mmp) REVERT: A 229 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8563 (tm-30) REVERT: A 242 SER cc_start: 0.8641 (p) cc_final: 0.8372 (t) REVERT: A 306 TRP cc_start: 0.7185 (p-90) cc_final: 0.6720 (m-10) REVERT: A 313 LEU cc_start: 0.8445 (mm) cc_final: 0.8145 (tp) REVERT: A 314 LYS cc_start: 0.7208 (tttm) cc_final: 0.6857 (mtpt) REVERT: A 385 TYR cc_start: 0.8023 (t80) cc_final: 0.7616 (t80) REVERT: A 392 GLU cc_start: 0.6243 (pt0) cc_final: 0.4394 (tt0) REVERT: A 410 TYR cc_start: 0.8464 (t80) cc_final: 0.7895 (t80) REVERT: A 493 GLU cc_start: 0.6496 (tt0) cc_final: 0.6078 (tt0) REVERT: A 494 GLU cc_start: 0.8151 (tp30) cc_final: 0.7710 (tt0) REVERT: A 563 LEU cc_start: 0.8549 (pt) cc_final: 0.6582 (tt) REVERT: B 113 TYR cc_start: 0.7675 (m-10) cc_final: 0.7465 (m-10) REVERT: B 133 THR cc_start: 0.7784 (p) cc_final: 0.7533 (p) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1550 time to fit residues: 36.7905 Evaluate side-chains 147 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.0370 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN C 111 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6326 Z= 0.156 Angle : 0.634 11.734 8619 Z= 0.316 Chirality : 0.040 0.152 966 Planarity : 0.004 0.070 1048 Dihedral : 7.618 77.055 961 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.31), residues: 758 helix: 0.55 (0.27), residues: 368 sheet: -2.20 (0.46), residues: 101 loop : -1.80 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 306 HIS 0.012 0.002 HIS C 111 PHE 0.019 0.001 PHE A 536 TYR 0.015 0.001 TYR A 185 ARG 0.005 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7564 (tmtt) cc_final: 0.7273 (tptp) REVERT: A 107 TYR cc_start: 0.8031 (t80) cc_final: 0.7673 (t80) REVERT: A 180 MET cc_start: 0.8940 (mmp) cc_final: 0.8374 (mmp) REVERT: A 229 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8565 (tm-30) REVERT: A 242 SER cc_start: 0.8643 (p) cc_final: 0.8337 (t) REVERT: A 313 LEU cc_start: 0.8496 (mm) cc_final: 0.8109 (tp) REVERT: A 314 LYS cc_start: 0.7200 (tttm) cc_final: 0.6807 (mtpt) REVERT: A 410 TYR cc_start: 0.8347 (t80) cc_final: 0.7821 (t80) REVERT: A 417 MET cc_start: 0.4719 (tpp) cc_final: 0.3882 (tpp) REVERT: A 494 GLU cc_start: 0.8199 (tp30) cc_final: 0.7684 (tt0) REVERT: A 528 MET cc_start: 0.7794 (ttm) cc_final: 0.7566 (ttm) REVERT: A 563 LEU cc_start: 0.8647 (pt) cc_final: 0.6634 (tt) REVERT: C 75 TYR cc_start: 0.8014 (t80) cc_final: 0.7797 (t80) REVERT: B 113 TYR cc_start: 0.7588 (m-10) cc_final: 0.7361 (m-10) REVERT: B 133 THR cc_start: 0.7852 (p) cc_final: 0.7626 (p) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1569 time to fit residues: 35.5735 Evaluate side-chains 148 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 52 optimal weight: 0.0050 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6326 Z= 0.188 Angle : 0.643 10.285 8619 Z= 0.326 Chirality : 0.041 0.161 966 Planarity : 0.004 0.077 1048 Dihedral : 7.906 89.455 961 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.31), residues: 758 helix: 0.55 (0.27), residues: 368 sheet: -2.15 (0.46), residues: 100 loop : -1.59 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 458 HIS 0.003 0.001 HIS C 111 PHE 0.027 0.002 PHE C 82 TYR 0.013 0.001 TYR B 114 ARG 0.004 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7524 (tmtt) cc_final: 0.7140 (tptp) REVERT: A 107 TYR cc_start: 0.8062 (t80) cc_final: 0.7731 (t80) REVERT: A 180 MET cc_start: 0.8908 (mmp) cc_final: 0.8319 (mmp) REVERT: A 229 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8576 (tm-30) REVERT: A 242 SER cc_start: 0.8627 (p) cc_final: 0.8382 (t) REVERT: A 313 LEU cc_start: 0.8512 (mm) cc_final: 0.8111 (tp) REVERT: A 314 LYS cc_start: 0.7205 (tttm) cc_final: 0.6808 (mtpt) REVERT: A 410 TYR cc_start: 0.8245 (t80) cc_final: 0.7683 (t80) REVERT: A 493 GLU cc_start: 0.6981 (tt0) cc_final: 0.5894 (tt0) REVERT: A 494 GLU cc_start: 0.8359 (tp30) cc_final: 0.7765 (tt0) REVERT: A 528 MET cc_start: 0.7838 (ttm) cc_final: 0.7571 (ttm) REVERT: A 563 LEU cc_start: 0.8677 (pt) cc_final: 0.6660 (tt) REVERT: C 75 TYR cc_start: 0.8113 (t80) cc_final: 0.7884 (t80) REVERT: B 133 THR cc_start: 0.7810 (p) cc_final: 0.7580 (p) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1714 time to fit residues: 38.7481 Evaluate side-chains 141 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6326 Z= 0.191 Angle : 0.659 10.470 8619 Z= 0.333 Chirality : 0.042 0.174 966 Planarity : 0.004 0.074 1048 Dihedral : 8.022 89.702 961 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.31), residues: 758 helix: 0.55 (0.27), residues: 366 sheet: -2.26 (0.47), residues: 101 loop : -1.53 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 541 HIS 0.006 0.001 HIS C 111 PHE 0.030 0.002 PHE A 287 TYR 0.019 0.002 TYR A 267 ARG 0.003 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7561 (tmtt) cc_final: 0.7242 (tptp) REVERT: A 180 MET cc_start: 0.8939 (mmp) cc_final: 0.8344 (mmp) REVERT: A 229 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8586 (tm-30) REVERT: A 242 SER cc_start: 0.8662 (p) cc_final: 0.8397 (t) REVERT: A 313 LEU cc_start: 0.8609 (mm) cc_final: 0.8152 (tp) REVERT: A 314 LYS cc_start: 0.7199 (tttm) cc_final: 0.6916 (ttpp) REVERT: A 410 TYR cc_start: 0.8261 (t80) cc_final: 0.7919 (t80) REVERT: A 417 MET cc_start: 0.4908 (tpp) cc_final: 0.4155 (tpp) REVERT: A 493 GLU cc_start: 0.7024 (tt0) cc_final: 0.6064 (tt0) REVERT: A 494 GLU cc_start: 0.8385 (tp30) cc_final: 0.7882 (tt0) REVERT: A 528 MET cc_start: 0.7875 (ttm) cc_final: 0.7625 (ttm) REVERT: A 563 LEU cc_start: 0.8697 (pt) cc_final: 0.6751 (tt) REVERT: C 75 TYR cc_start: 0.8192 (t80) cc_final: 0.7944 (t80) REVERT: B 108 GLU cc_start: 0.7688 (pp20) cc_final: 0.7481 (pp20) REVERT: B 133 THR cc_start: 0.7836 (p) cc_final: 0.7610 (p) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1797 time to fit residues: 41.3485 Evaluate side-chains 142 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 0.0980 chunk 60 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 HIS ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6326 Z= 0.190 Angle : 0.654 10.590 8619 Z= 0.330 Chirality : 0.042 0.149 966 Planarity : 0.005 0.078 1048 Dihedral : 7.728 83.092 961 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.31), residues: 758 helix: 0.62 (0.27), residues: 367 sheet: -2.31 (0.47), residues: 101 loop : -1.52 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 541 HIS 0.016 0.002 HIS C 111 PHE 0.027 0.002 PHE A 287 TYR 0.021 0.002 TYR A 267 ARG 0.003 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7467 (tmtt) cc_final: 0.7056 (tptp) REVERT: A 180 MET cc_start: 0.8950 (mmp) cc_final: 0.8422 (mmp) REVERT: A 229 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8569 (tm-30) REVERT: A 242 SER cc_start: 0.8646 (p) cc_final: 0.8390 (t) REVERT: A 313 LEU cc_start: 0.8671 (mm) cc_final: 0.8174 (tt) REVERT: A 314 LYS cc_start: 0.7242 (tttm) cc_final: 0.6946 (ttpp) REVERT: A 410 TYR cc_start: 0.8137 (t80) cc_final: 0.7843 (t80) REVERT: A 494 GLU cc_start: 0.8425 (tp30) cc_final: 0.7877 (tt0) REVERT: A 563 LEU cc_start: 0.8702 (pt) cc_final: 0.6745 (tt) REVERT: C 75 TYR cc_start: 0.8219 (t80) cc_final: 0.7973 (t80) REVERT: B 108 GLU cc_start: 0.7702 (pp20) cc_final: 0.7488 (pp20) REVERT: B 133 THR cc_start: 0.7844 (p) cc_final: 0.7613 (p) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1409 time to fit residues: 30.9112 Evaluate side-chains 140 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6326 Z= 0.257 Angle : 0.715 12.358 8619 Z= 0.364 Chirality : 0.044 0.161 966 Planarity : 0.005 0.083 1048 Dihedral : 7.493 68.775 961 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.31), residues: 758 helix: 0.40 (0.27), residues: 367 sheet: -2.46 (0.49), residues: 94 loop : -1.57 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 271 HIS 0.008 0.002 HIS A 143 PHE 0.020 0.002 PHE A 536 TYR 0.024 0.002 TYR B 52 ARG 0.004 0.001 ARG B 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7500 (tmtt) cc_final: 0.7151 (tptp) REVERT: A 107 TYR cc_start: 0.7936 (t80) cc_final: 0.7668 (t80) REVERT: A 180 MET cc_start: 0.8981 (mmp) cc_final: 0.8515 (mmp) REVERT: A 229 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8577 (tm-30) REVERT: A 242 SER cc_start: 0.8750 (p) cc_final: 0.8508 (t) REVERT: A 313 LEU cc_start: 0.8747 (mm) cc_final: 0.8158 (tt) REVERT: A 314 LYS cc_start: 0.7300 (tttm) cc_final: 0.6944 (ttpp) REVERT: A 410 TYR cc_start: 0.8283 (t80) cc_final: 0.8030 (t80) REVERT: A 494 GLU cc_start: 0.8479 (tp30) cc_final: 0.7869 (tt0) REVERT: A 563 LEU cc_start: 0.8818 (pt) cc_final: 0.6910 (tt) REVERT: C 75 TYR cc_start: 0.8287 (t80) cc_final: 0.8015 (t80) REVERT: B 108 GLU cc_start: 0.7684 (pp20) cc_final: 0.7425 (pp20) REVERT: B 120 VAL cc_start: 0.7686 (m) cc_final: 0.7408 (p) REVERT: B 124 TYR cc_start: 0.8604 (p90) cc_final: 0.8394 (p90) REVERT: B 133 THR cc_start: 0.7899 (p) cc_final: 0.7670 (p) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1460 time to fit residues: 33.0873 Evaluate side-chains 139 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.0370 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 59 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN B 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.180347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.160735 restraints weight = 11318.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.165113 restraints weight = 7154.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.168228 restraints weight = 4914.204| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6326 Z= 0.167 Angle : 0.650 10.397 8619 Z= 0.328 Chirality : 0.042 0.161 966 Planarity : 0.004 0.079 1048 Dihedral : 7.107 67.124 961 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.32), residues: 758 helix: 0.69 (0.27), residues: 365 sheet: -2.55 (0.46), residues: 102 loop : -1.27 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 541 HIS 0.009 0.001 HIS C 111 PHE 0.035 0.002 PHE A 427 TYR 0.017 0.002 TYR B 52 ARG 0.003 0.000 ARG A 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1852.74 seconds wall clock time: 33 minutes 26.23 seconds (2006.23 seconds total)