Starting phenix.real_space_refine on Fri Sep 11 01:17:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vrk_21369/09_2026/6vrk_21369.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vrk_21369/09_2026/6vrk_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/cci-nas-00/data/ceres_data/6vrk_21369/09_2026/6vrk_21369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vrk_21369/09_2026/6vrk_21369.map" model { file = "/net/cci-nas-00/data/ceres_data/6vrk_21369/09_2026/6vrk_21369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vrk_21369/09_2026/6vrk_21369.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vrk_21369/09_2026/6vrk_21369.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vrk_21369/09_2026/6vrk_21369.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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 chiralities: 2 Time building chain proxies: 1.66, per 1000 atoms: 0.27 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: 0.59 Conformation dependent library (CDL) restraints added in 494.3 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: 0.11 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: 0.78 Time building geometry restraints manager: 0.78 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: 3239 17.44 - 34.87: 295 34.87 - 52.31: 46 52.31 - 69.75: 11 69.75 - 87.18: 9 Dihedral angle restraints: 3600 sinusoidal: 1386 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 3597 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: 7.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.850 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 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 6331 Z= 0.200 Angle : 0.688 11.612 8631 Z= 0.351 Chirality : 0.040 0.208 966 Planarity : 0.004 0.065 1048 Dihedral : 13.942 87.184 2185 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.65 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 152 TYR 0.014 0.001 TYR B 123 PHE 0.021 0.001 PHE A 548 TRP 0.007 0.001 TRP A 103 HIS 0.005 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.20 ( 6326) covalent geometry : angle 0.68599 / 0.35 ( 8619) SS BOND : bond 0.00144 / 0.08 ( 3) SS BOND : angle 2.27138 / 1.19 ( 6) hydrogen bonds : bond 0.15893 / 10.11 ( 304) hydrogen bonds : angle 6.33585 / 4.49 ( 855) link_NAG-ASN : bond 0.00170 / 0.11 ( 2) link_NAG-ASN : angle 0.72521 / 0.41 ( 6) *********************** 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 to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.178 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: 0.0662 time to fit residues: 19.1054 Evaluate side-chains 159 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 238 GLN A 240 HIS ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN C 109 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.185928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.165815 restraints weight = 11789.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.170407 restraints weight = 7160.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.173667 restraints weight = 4825.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.175942 restraints weight = 3483.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.177681 restraints weight = 2665.776| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6331 Z= 0.122 Angle : 0.624 13.825 8631 Z= 0.315 Chirality : 0.040 0.158 966 Planarity : 0.004 0.077 1048 Dihedral : 7.689 65.471 869 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.31 % Allowed : 4.62 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.29), residues: 758 helix: -0.09 (0.26), residues: 367 sheet: -2.54 (0.46), residues: 86 loop : -2.60 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 152 TYR 0.014 0.001 TYR B 52 PHE 0.023 0.001 PHE A 548 TRP 0.030 0.001 TRP A 541 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6326) covalent geometry : angle 0.62212 / 0.31 ( 8619) SS BOND : bond 0.00468 / 0.27 ( 3) SS BOND : angle 1.98029 / 1.03 ( 6) hydrogen bonds : bond 0.03860 / 2.53 ( 304) hydrogen bonds : angle 4.92485 / 3.52 ( 855) link_NAG-ASN : bond 0.00492 / 0.30 ( 2) link_NAG-ASN : angle 0.65482 / 0.37 ( 6) *********************** 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 183 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7679 (tmtt) cc_final: 0.7368 (tptp) REVERT: A 107 TYR cc_start: 0.7804 (t80) cc_final: 0.7457 (t80) REVERT: A 180 MET cc_start: 0.8786 (mmp) cc_final: 0.8506 (mmp) REVERT: A 242 SER cc_start: 0.8386 (p) cc_final: 0.8155 (t) REVERT: A 417 MET cc_start: 0.6466 (mtm) cc_final: 0.6091 (mtm) REVERT: A 493 GLU cc_start: 0.6437 (tt0) cc_final: 0.6107 (mt-10) REVERT: A 563 LEU cc_start: 0.8438 (pt) cc_final: 0.7457 (tt) REVERT: B 109 ASP cc_start: 0.7323 (m-30) cc_final: 0.7086 (m-30) outliers start: 2 outliers final: 1 residues processed: 182 average time/residue: 0.0638 time to fit residues: 16.1880 Evaluate side-chains 152 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 0.0470 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 238 GLN A 240 HIS ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN C 28 HIS C 111 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.188156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168363 restraints weight = 11757.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.172811 restraints weight = 7287.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.175951 restraints weight = 4977.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.178255 restraints weight = 3633.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.179703 restraints weight = 2782.240| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6331 Z= 0.118 Angle : 0.630 14.162 8631 Z= 0.314 Chirality : 0.040 0.155 966 Planarity : 0.004 0.076 1048 Dihedral : 7.319 62.198 869 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.30), residues: 758 helix: 0.28 (0.27), residues: 369 sheet: -2.46 (0.47), residues: 93 loop : -2.28 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 390 TYR 0.016 0.001 TYR B 52 PHE 0.030 0.002 PHE A 287 TRP 0.019 0.001 TRP A 541 HIS 0.002 0.001 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 6326) covalent geometry : angle 0.62802 / 0.31 ( 8619) SS BOND : bond 0.00797 / 0.46 ( 3) SS BOND : angle 1.88044 / 1.01 ( 6) hydrogen bonds : bond 0.03465 / 2.30 ( 304) hydrogen bonds : angle 4.69518 / 3.36 ( 855) link_NAG-ASN : bond 0.00187 / 0.11 ( 2) link_NAG-ASN : angle 0.83806 / 0.46 ( 6) *********************** 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 173 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7602 (tmtt) cc_final: 0.7269 (tptp) REVERT: A 107 TYR cc_start: 0.7821 (t80) cc_final: 0.7466 (t80) REVERT: A 152 ARG cc_start: 0.6949 (ttp-110) cc_final: 0.6104 (ttm-80) REVERT: A 180 MET cc_start: 0.8777 (mmp) cc_final: 0.8413 (mmp) REVERT: A 187 LEU cc_start: 0.8903 (tp) cc_final: 0.8703 (tp) REVERT: A 229 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8530 (tm-30) REVERT: A 242 SER cc_start: 0.8457 (p) cc_final: 0.8132 (t) REVERT: A 306 TRP cc_start: 0.7123 (p-90) cc_final: 0.6708 (m-10) REVERT: A 313 LEU cc_start: 0.8583 (mm) cc_final: 0.8106 (tt) REVERT: A 410 TYR cc_start: 0.8544 (t80) cc_final: 0.8129 (t80) REVERT: A 493 GLU cc_start: 0.6483 (tt0) cc_final: 0.6273 (tt0) REVERT: A 563 LEU cc_start: 0.8396 (pt) cc_final: 0.7403 (tt) REVERT: C 107 TYR cc_start: 0.7054 (m-80) cc_final: 0.6701 (m-10) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.0712 time to fit residues: 16.7282 Evaluate side-chains 145 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 36 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 0.0570 chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 HIS ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.188346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.168857 restraints weight = 12036.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.173152 restraints weight = 7647.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.176167 restraints weight = 5307.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.178157 restraints weight = 3924.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.179790 restraints weight = 3075.858| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6331 Z= 0.118 Angle : 0.647 17.084 8631 Z= 0.317 Chirality : 0.040 0.229 966 Planarity : 0.004 0.071 1048 Dihedral : 7.179 73.148 869 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.30), residues: 758 helix: 0.43 (0.27), residues: 365 sheet: -2.36 (0.46), residues: 101 loop : -1.97 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.019 0.001 TYR B 114 PHE 0.038 0.002 PHE A 373 TRP 0.025 0.001 TRP A 306 HIS 0.006 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 6326) covalent geometry : angle 0.64555 / 0.32 ( 8619) SS BOND : bond 0.00351 / 0.20 ( 3) SS BOND : angle 1.61911 / 0.88 ( 6) hydrogen bonds : bond 0.03401 / 2.31 ( 304) hydrogen bonds : angle 4.66029 / 3.33 ( 855) link_NAG-ASN : bond 0.00210 / 0.13 ( 2) link_NAG-ASN : angle 0.71337 / 0.40 ( 6) *********************** 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 173 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7660 (tmtt) cc_final: 0.7306 (tptp) REVERT: A 88 PHE cc_start: 0.8233 (t80) cc_final: 0.8023 (t80) REVERT: A 107 TYR cc_start: 0.7858 (t80) cc_final: 0.7532 (t80) REVERT: A 152 ARG cc_start: 0.6915 (ttp-110) cc_final: 0.6087 (ttm-80) REVERT: A 229 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8504 (tm-30) REVERT: A 242 SER cc_start: 0.8472 (p) cc_final: 0.8200 (t) REVERT: A 313 LEU cc_start: 0.8499 (mm) cc_final: 0.8170 (tp) REVERT: A 410 TYR cc_start: 0.8473 (t80) cc_final: 0.8043 (t80) REVERT: A 493 GLU cc_start: 0.6551 (tt0) cc_final: 0.6205 (tt0) REVERT: A 494 GLU cc_start: 0.8071 (tp30) cc_final: 0.7781 (tp30) REVERT: A 558 MET cc_start: 0.6692 (mtp) cc_final: 0.6474 (mtt) REVERT: A 563 LEU cc_start: 0.8379 (pt) cc_final: 0.7468 (tt) REVERT: C 118 PHE cc_start: 0.8470 (m-80) cc_final: 0.8139 (m-10) REVERT: B 108 GLU cc_start: 0.7860 (pp20) cc_final: 0.7643 (pp20) REVERT: B 133 THR cc_start: 0.7739 (p) cc_final: 0.7482 (p) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.0624 time to fit residues: 14.8566 Evaluate side-chains 146 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 7 optimal weight: 0.0050 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 HIS ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS B 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.187552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.167764 restraints weight = 12074.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.172156 restraints weight = 7634.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.175294 restraints weight = 5285.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.177410 restraints weight = 3878.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.179154 restraints weight = 3019.627| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6331 Z= 0.113 Angle : 0.618 11.300 8631 Z= 0.308 Chirality : 0.040 0.161 966 Planarity : 0.004 0.073 1048 Dihedral : 7.230 79.445 869 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.30), residues: 758 helix: 0.54 (0.27), residues: 367 sheet: -2.23 (0.47), residues: 101 loop : -1.85 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 117 TYR 0.016 0.001 TYR B 114 PHE 0.018 0.001 PHE C 118 TRP 0.018 0.001 TRP A 458 HIS 0.012 0.002 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 6326) covalent geometry : angle 0.61756 / 0.31 ( 8619) SS BOND : bond 0.00355 / 0.20 ( 3) SS BOND : angle 1.19156 / 0.64 ( 6) hydrogen bonds : bond 0.03370 / 2.26 ( 304) hydrogen bonds : angle 4.58329 / 3.28 ( 855) link_NAG-ASN : bond 0.00213 / 0.13 ( 2) link_NAG-ASN : angle 0.74738 / 0.41 ( 6) *********************** 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 to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7646 (tmtt) cc_final: 0.7288 (tptp) REVERT: A 88 PHE cc_start: 0.8272 (t80) cc_final: 0.8072 (t80) REVERT: A 152 ARG cc_start: 0.6923 (ttp-110) cc_final: 0.6039 (ttm-80) REVERT: A 180 MET cc_start: 0.8874 (mmp) cc_final: 0.8540 (mmt) REVERT: A 187 LEU cc_start: 0.8810 (tp) cc_final: 0.8603 (tp) REVERT: A 229 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8536 (tm-30) REVERT: A 242 SER cc_start: 0.8566 (p) cc_final: 0.8250 (t) REVERT: A 313 LEU cc_start: 0.8375 (mm) cc_final: 0.8019 (tp) REVERT: A 314 LYS cc_start: 0.7218 (tttm) cc_final: 0.6845 (mtpt) REVERT: A 410 TYR cc_start: 0.8366 (t80) cc_final: 0.7746 (t80) REVERT: A 417 MET cc_start: 0.4494 (tpp) cc_final: 0.3578 (tpp) REVERT: A 432 ILE cc_start: 0.8798 (mt) cc_final: 0.8511 (mt) REVERT: A 562 GLN cc_start: 0.6825 (tp-100) cc_final: 0.6526 (tp40) REVERT: A 563 LEU cc_start: 0.8457 (pt) cc_final: 0.7349 (tt) REVERT: B 108 GLU cc_start: 0.7787 (pp20) cc_final: 0.7567 (pp20) REVERT: B 133 THR cc_start: 0.7730 (p) cc_final: 0.7484 (p) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0560 time to fit residues: 13.5602 Evaluate side-chains 144 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 29 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 69 optimal weight: 0.0010 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.185231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.165465 restraints weight = 11596.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.169736 restraints weight = 7379.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.172867 restraints weight = 5143.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.175134 restraints weight = 3787.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.176821 restraints weight = 2916.228| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6331 Z= 0.117 Angle : 0.623 11.691 8631 Z= 0.312 Chirality : 0.040 0.160 966 Planarity : 0.004 0.076 1048 Dihedral : 7.253 82.203 869 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.31), residues: 758 helix: 0.57 (0.27), residues: 369 sheet: -2.12 (0.48), residues: 101 loop : -1.77 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 117 TYR 0.014 0.001 TYR A 185 PHE 0.019 0.001 PHE C 118 TRP 0.041 0.002 TRP A 271 HIS 0.004 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 6326) covalent geometry : angle 0.62212 / 0.31 ( 8619) SS BOND : bond 0.00368 / 0.20 ( 3) SS BOND : angle 1.17216 / 0.62 ( 6) hydrogen bonds : bond 0.03273 / 2.19 ( 304) hydrogen bonds : angle 4.58585 / 3.27 ( 855) link_NAG-ASN : bond 0.00179 / 0.11 ( 2) link_NAG-ASN : angle 0.81544 / 0.45 ( 6) *********************** 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 171 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7599 (tmtt) cc_final: 0.7179 (tptp) REVERT: A 180 MET cc_start: 0.8939 (mmp) cc_final: 0.8615 (mmt) REVERT: A 229 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8586 (tm-30) REVERT: A 242 SER cc_start: 0.8584 (p) cc_final: 0.8256 (t) REVERT: A 313 LEU cc_start: 0.8453 (mm) cc_final: 0.7940 (tp) REVERT: A 314 LYS cc_start: 0.7220 (tttm) cc_final: 0.6814 (mtpt) REVERT: A 410 TYR cc_start: 0.8279 (t80) cc_final: 0.7712 (t80) REVERT: A 417 MET cc_start: 0.4837 (tpp) cc_final: 0.4447 (tpp) REVERT: A 432 ILE cc_start: 0.8850 (mt) cc_final: 0.8569 (mt) REVERT: A 493 GLU cc_start: 0.7369 (tt0) cc_final: 0.6121 (tt0) REVERT: A 563 LEU cc_start: 0.8547 (pt) cc_final: 0.7480 (tt) REVERT: B 133 THR cc_start: 0.7777 (p) cc_final: 0.7534 (p) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.0643 time to fit residues: 15.4283 Evaluate side-chains 145 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 0.0070 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN A 112 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** 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 = 0.4262 r_free = 0.4262 target = 0.186970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.167179 restraints weight = 11562.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.171593 restraints weight = 7341.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.174777 restraints weight = 5063.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.177002 restraints weight = 3695.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.178680 restraints weight = 2850.497| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6331 Z= 0.112 Angle : 0.625 10.851 8631 Z= 0.313 Chirality : 0.041 0.163 966 Planarity : 0.004 0.073 1048 Dihedral : 6.977 78.296 869 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.31), residues: 758 helix: 0.65 (0.27), residues: 368 sheet: -1.94 (0.48), residues: 101 loop : -1.68 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 79 TYR 0.018 0.001 TYR A 267 PHE 0.018 0.001 PHE A 536 TRP 0.020 0.001 TRP A 458 HIS 0.005 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 6326) covalent geometry : angle 0.62339 / 0.31 ( 8619) SS BOND : bond 0.00367 / 0.21 ( 3) SS BOND : angle 1.35260 / 0.68 ( 6) hydrogen bonds : bond 0.03264 / 2.21 ( 304) hydrogen bonds : angle 4.64201 / 3.29 ( 855) link_NAG-ASN : bond 0.00160 / 0.10 ( 2) link_NAG-ASN : angle 1.11161 / 0.60 ( 6) *********************** 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 168 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7601 (tmtt) cc_final: 0.7233 (tptp) REVERT: A 144 ARG cc_start: 0.6982 (mtt180) cc_final: 0.6644 (mtt180) REVERT: A 180 MET cc_start: 0.8910 (mmp) cc_final: 0.8591 (mmt) REVERT: A 187 LEU cc_start: 0.8830 (tp) cc_final: 0.8621 (tp) REVERT: A 229 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8570 (tm-30) REVERT: A 242 SER cc_start: 0.8512 (p) cc_final: 0.8227 (t) REVERT: A 313 LEU cc_start: 0.8461 (mm) cc_final: 0.7980 (tp) REVERT: A 314 LYS cc_start: 0.7204 (tttm) cc_final: 0.6823 (mtpt) REVERT: A 410 TYR cc_start: 0.8125 (t80) cc_final: 0.7513 (t80) REVERT: A 417 MET cc_start: 0.4910 (tpp) cc_final: 0.4621 (tpp) REVERT: A 432 ILE cc_start: 0.8789 (mt) cc_final: 0.8446 (mt) REVERT: A 493 GLU cc_start: 0.7253 (tt0) cc_final: 0.6065 (tt0) REVERT: A 563 LEU cc_start: 0.8484 (pt) cc_final: 0.7101 (tt) REVERT: C 109 GLN cc_start: 0.7144 (tt0) cc_final: 0.6507 (tt0) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0619 time to fit residues: 14.5692 Evaluate side-chains 143 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.0040 chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.179030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.159268 restraints weight = 11840.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.163456 restraints weight = 7400.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.166542 restraints weight = 5137.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.168743 restraints weight = 3788.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.170455 restraints weight = 2928.900| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6331 Z= 0.192 Angle : 0.725 14.014 8631 Z= 0.367 Chirality : 0.044 0.175 966 Planarity : 0.005 0.077 1048 Dihedral : 6.774 50.230 869 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.30), residues: 758 helix: 0.36 (0.26), residues: 368 sheet: -2.10 (0.52), residues: 90 loop : -1.65 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 307 TYR 0.020 0.002 TYR A 267 PHE 0.027 0.002 PHE C 82 TRP 0.024 0.002 TRP A 541 HIS 0.018 0.003 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 ( 6326) covalent geometry : angle 0.72216 / 0.37 ( 8619) SS BOND : bond 0.00798 / 0.45 ( 3) SS BOND : angle 2.45962 / 1.36 ( 6) hydrogen bonds : bond 0.03813 / 2.48 ( 304) hydrogen bonds : angle 4.98646 / 3.53 ( 855) link_NAG-ASN : bond 0.00082 / 0.05 ( 2) link_NAG-ASN : angle 1.31966 / 0.72 ( 6) *********************** 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 164 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7645 (tmtt) cc_final: 0.7304 (tptp) REVERT: A 144 ARG cc_start: 0.7084 (mtt180) cc_final: 0.6746 (mtt-85) REVERT: A 229 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8551 (tm-30) REVERT: A 242 SER cc_start: 0.8687 (p) cc_final: 0.8433 (t) REVERT: A 314 LYS cc_start: 0.7308 (tttm) cc_final: 0.7033 (ttpp) REVERT: A 410 TYR cc_start: 0.8329 (t80) cc_final: 0.7924 (t80) REVERT: A 417 MET cc_start: 0.5063 (tpp) cc_final: 0.4666 (tpp) REVERT: A 563 LEU cc_start: 0.8614 (pt) cc_final: 0.7527 (tt) REVERT: C 109 GLN cc_start: 0.7241 (tt0) cc_final: 0.6805 (tt0) REVERT: B 108 GLU cc_start: 0.7637 (pp20) cc_final: 0.7395 (pp20) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0597 time to fit residues: 13.9318 Evaluate side-chains 137 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 74 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN C 111 HIS B 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.182677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.162986 restraints weight = 11759.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.167299 restraints weight = 7393.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.170399 restraints weight = 5113.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.172617 restraints weight = 3766.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.174096 restraints weight = 2907.490| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6331 Z= 0.121 Angle : 0.678 13.220 8631 Z= 0.333 Chirality : 0.043 0.164 966 Planarity : 0.004 0.078 1048 Dihedral : 6.539 48.906 869 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.15 % Allowed : 0.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.31), residues: 758 helix: 0.41 (0.26), residues: 374 sheet: -2.16 (0.52), residues: 92 loop : -1.64 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 307 TYR 0.022 0.001 TYR A 267 PHE 0.020 0.001 PHE A 536 TRP 0.048 0.002 TRP A 271 HIS 0.009 0.002 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 6326) covalent geometry : angle 0.67605 / 0.33 ( 8619) SS BOND : bond 0.00420 / 0.23 ( 3) SS BOND : angle 1.71348 / 0.92 ( 6) hydrogen bonds : bond 0.03395 / 2.28 ( 304) hydrogen bonds : angle 4.89357 / 3.43 ( 855) link_NAG-ASN : bond 0.00252 / 0.16 ( 2) link_NAG-ASN : angle 1.07343 / 0.58 ( 6) *********************** 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 167 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7618 (tmtt) cc_final: 0.7244 (tptp) REVERT: A 144 ARG cc_start: 0.6896 (mtt180) cc_final: 0.6578 (mtt-85) REVERT: A 180 MET cc_start: 0.8884 (mmp) cc_final: 0.8328 (mmp) REVERT: A 229 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8566 (tm-30) REVERT: A 242 SER cc_start: 0.8498 (p) cc_final: 0.8241 (t) REVERT: A 313 LEU cc_start: 0.8518 (mm) cc_final: 0.8173 (tp) REVERT: A 314 LYS cc_start: 0.7224 (tttm) cc_final: 0.6993 (ttpp) REVERT: A 410 TYR cc_start: 0.8104 (t80) cc_final: 0.7785 (t80) REVERT: A 432 ILE cc_start: 0.8808 (mt) cc_final: 0.8568 (mt) REVERT: A 563 LEU cc_start: 0.8472 (pt) cc_final: 0.7401 (tt) REVERT: B 108 GLU cc_start: 0.7587 (pp20) cc_final: 0.7385 (pp20) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.0623 time to fit residues: 14.6505 Evaluate side-chains 142 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 45 optimal weight: 0.0570 chunk 3 optimal weight: 4.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN B 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.179934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.160353 restraints weight = 11500.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.164794 restraints weight = 7206.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.167979 restraints weight = 4925.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.170311 restraints weight = 3574.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.171906 restraints weight = 2713.101| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6331 Z= 0.121 Angle : 0.653 11.967 8631 Z= 0.325 Chirality : 0.042 0.160 966 Planarity : 0.004 0.079 1048 Dihedral : 6.437 48.142 869 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.15 % Allowed : 0.62 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.31), residues: 758 helix: 0.60 (0.27), residues: 369 sheet: -2.11 (0.52), residues: 93 loop : -1.41 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.028 0.002 TYR A 267 PHE 0.023 0.001 PHE A 287 TRP 0.024 0.001 TRP A 458 HIS 0.005 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6326) covalent geometry : angle 0.65197 / 0.32 ( 8619) SS BOND : bond 0.00397 / 0.21 ( 3) SS BOND : angle 1.57769 / 0.84 ( 6) hydrogen bonds : bond 0.03382 / 2.26 ( 304) hydrogen bonds : angle 4.76116 / 3.35 ( 855) link_NAG-ASN : bond 0.00250 / 0.16 ( 2) link_NAG-ASN : angle 0.99878 / 0.54 ( 6) ********************** 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 161 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7548 (tmtt) cc_final: 0.7211 (tptp) REVERT: A 144 ARG cc_start: 0.6954 (mtt180) cc_final: 0.6641 (mtt-85) REVERT: A 180 MET cc_start: 0.8898 (mmp) cc_final: 0.8326 (mmp) REVERT: A 229 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8587 (tm-30) REVERT: A 242 SER cc_start: 0.8486 (p) cc_final: 0.8178 (t) REVERT: A 313 LEU cc_start: 0.8511 (mm) cc_final: 0.8057 (tt) REVERT: A 314 LYS cc_start: 0.7207 (tttm) cc_final: 0.6935 (ttpp) REVERT: A 410 TYR cc_start: 0.8173 (t80) cc_final: 0.7894 (t80) REVERT: A 432 ILE cc_start: 0.8783 (mt) cc_final: 0.8529 (mt) REVERT: A 467 LEU cc_start: 0.7973 (mt) cc_final: 0.7749 (tt) REVERT: A 562 GLN cc_start: 0.6786 (tp-100) cc_final: 0.6560 (tp40) REVERT: A 563 LEU cc_start: 0.8450 (pt) cc_final: 0.7262 (tt) REVERT: B 124 TYR cc_start: 0.8230 (p90) cc_final: 0.7977 (p90) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.0614 time to fit residues: 14.0032 Evaluate side-chains 139 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 53 optimal weight: 0.0970 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.184017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.164144 restraints weight = 11665.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.168290 restraints weight = 7522.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.171425 restraints weight = 5307.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.173684 restraints weight = 3947.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.175449 restraints weight = 3080.459| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6331 Z= 0.114 Angle : 0.651 11.134 8631 Z= 0.326 Chirality : 0.042 0.147 966 Planarity : 0.004 0.078 1048 Dihedral : 6.379 48.861 869 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.15 % Allowed : 0.62 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.31), residues: 758 helix: 0.71 (0.27), residues: 367 sheet: -2.10 (0.53), residues: 92 loop : -1.40 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.017 0.001 TYR A 142 PHE 0.011 0.001 PHE A 536 TRP 0.074 0.002 TRP A 541 HIS 0.008 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 6326) covalent geometry : angle 0.64988 / 0.33 ( 8619) SS BOND : bond 0.00372 / 0.20 ( 3) SS BOND : angle 1.46088 / 0.79 ( 6) hydrogen bonds : bond 0.03310 / 2.23 ( 304) hydrogen bonds : angle 4.82538 / 3.40 ( 855) link_NAG-ASN : bond 0.00236 / 0.15 ( 2) link_NAG-ASN : angle 0.90684 / 0.50 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1243.96 seconds wall clock time: 22 minutes 12.53 seconds (1332.53 seconds total)