Starting phenix.real_space_refine on Fri Dec 27 19:34:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewy_50026/12_2024/9ewy_50026.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewy_50026/12_2024/9ewy_50026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ewy_50026/12_2024/9ewy_50026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewy_50026/12_2024/9ewy_50026.map" model { file = "/net/cci-nas-00/data/ceres_data/9ewy_50026/12_2024/9ewy_50026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewy_50026/12_2024/9ewy_50026.cif" } resolution = 3.1 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 27 5.16 5 C 4116 2.51 5 N 1168 2.21 5 O 1181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6496 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6441 Classifications: {'peptide': 815} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 781} Chain breaks: 4 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {' ZN': 2, 'FAD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4700 SG CYS A 697 48.096 60.475 86.700 1.00 99.64 S ATOM 4719 SG CYS A 700 51.349 61.564 85.009 1.00105.81 S ATOM 4895 SG CYS A 721 48.875 59.472 82.989 1.00 91.96 S ATOM 4923 SG CYS A 724 46.598 45.990 79.356 1.00104.20 S ATOM 4946 SG CYS A 727 46.101 46.259 75.609 1.00107.09 S ATOM 5106 SG CYS A 747 43.417 44.556 77.806 1.00109.57 S Time building chain proxies: 4.83, per 1000 atoms: 0.74 Number of scatterers: 6496 At special positions: 0 Unit cell: (74.226, 100.914, 120.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 27 16.00 P 2 15.00 O 1181 8.00 N 1168 7.00 C 4116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 926.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" ND1 HIS A 718 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 700 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 697 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 721 " pdb=" ZN A1103 " pdb="ZN ZN A1103 " - pdb=" ND1 HIS A 750 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 747 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 724 " Number of angles added : 6 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 55.7% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 Processing helix chain 'A' and resid 22 through 37 Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 61 through 72 Processing helix chain 'A' and resid 93 through 106 Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 266 through 277 removed outlier: 4.182A pdb=" N PHE A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 326 through 342 Processing helix chain 'A' and resid 392 through 395 Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 404 through 425 Processing helix chain 'A' and resid 428 through 441 Processing helix chain 'A' and resid 442 through 446 Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.557A pdb=" N TYR A 458 " --> pdb=" O VAL A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.003A pdb=" N ARG A 480 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP A 481 " --> pdb=" O GLN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 removed outlier: 3.912A pdb=" N GLU A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 3.952A pdb=" N CYS A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 562 Processing helix chain 'A' and resid 566 through 580 removed outlier: 3.662A pdb=" N ALA A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'A' and resid 596 through 611 Processing helix chain 'A' and resid 631 through 645 Processing helix chain 'A' and resid 908 through 959 Processing helix chain 'A' and resid 963 through 1015 removed outlier: 3.662A pdb=" N THR A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1061 removed outlier: 3.830A pdb=" N ARG A1035 " --> pdb=" O ASP A1031 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A1036 " --> pdb=" O GLN A1032 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A1061 " --> pdb=" O SER A1057 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 177 removed outlier: 6.647A pdb=" N LYS A 86 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE A 215 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU A 88 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ASP A 484 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 378 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 126 Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 185 removed outlier: 5.469A pdb=" N PHE A 181 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN A 199 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 183 " --> pdb=" O GLN A 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 229 through 232 Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.436A pdb=" N THR A 297 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE A 284 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL A 295 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR A 286 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR A 293 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS A 288 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR A 291 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 709 through 712 Processing sheet with id=AA7, first strand: chain 'A' and resid 736 through 739 removed outlier: 3.588A pdb=" N HIS A 744 " --> pdb=" O HIS A 739 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1059 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: 2.27 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2173 1.34 - 1.46: 1010 1.46 - 1.58: 3413 1.58 - 1.70: 2 1.70 - 1.82: 36 Bond restraints: 6634 Sorted by residual: bond pdb=" O3P FAD A1101 " pdb=" P FAD A1101 " ideal model delta sigma weight residual 1.660 1.584 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" O5' FAD A1101 " pdb=" P FAD A1101 " ideal model delta sigma weight residual 1.637 1.573 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O5B FAD A1101 " pdb=" PA FAD A1101 " ideal model delta sigma weight residual 1.634 1.574 0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" O3P FAD A1101 " pdb=" PA FAD A1101 " ideal model delta sigma weight residual 1.633 1.585 0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" O2P FAD A1101 " pdb=" P FAD A1101 " ideal model delta sigma weight residual 1.495 1.531 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 6629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 8844 1.63 - 3.27: 116 3.27 - 4.90: 20 4.90 - 6.54: 5 6.54 - 8.17: 4 Bond angle restraints: 8989 Sorted by residual: angle pdb=" O1P FAD A1101 " pdb=" P FAD A1101 " pdb=" O2P FAD A1101 " ideal model delta sigma weight residual 122.50 114.33 8.17 3.00e+00 1.11e-01 7.42e+00 angle pdb=" O1A FAD A1101 " pdb=" PA FAD A1101 " pdb=" O5B FAD A1101 " ideal model delta sigma weight residual 104.10 111.26 -7.16 3.00e+00 1.11e-01 5.69e+00 angle pdb=" C THR A 253 " pdb=" N GLN A 254 " pdb=" CA GLN A 254 " ideal model delta sigma weight residual 121.18 116.48 4.70 1.98e+00 2.55e-01 5.63e+00 angle pdb=" O1A FAD A1101 " pdb=" PA FAD A1101 " pdb=" O2A FAD A1101 " ideal model delta sigma weight residual 121.20 114.65 6.55 3.00e+00 1.11e-01 4.77e+00 angle pdb=" P FAD A1101 " pdb=" O3P FAD A1101 " pdb=" PA FAD A1101 " ideal model delta sigma weight residual 130.34 124.03 6.31 3.00e+00 1.11e-01 4.42e+00 ... (remaining 8984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3517 17.93 - 35.87: 372 35.87 - 53.80: 69 53.80 - 71.74: 17 71.74 - 89.67: 15 Dihedral angle restraints: 3990 sinusoidal: 1648 harmonic: 2342 Sorted by residual: dihedral pdb=" CB GLU A 449 " pdb=" CG GLU A 449 " pdb=" CD GLU A 449 " pdb=" OE1 GLU A 449 " ideal model delta sinusoidal sigma weight residual 0.00 89.67 -89.67 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 114 " pdb=" CG GLU A 114 " pdb=" CD GLU A 114 " pdb=" OE1 GLU A 114 " ideal model delta sinusoidal sigma weight residual 0.00 -89.05 89.05 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CG ARG A 709 " pdb=" CD ARG A 709 " pdb=" NE ARG A 709 " pdb=" CZ ARG A 709 " ideal model delta sinusoidal sigma weight residual 180.00 137.16 42.84 2 1.50e+01 4.44e-03 9.86e+00 ... (remaining 3987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 646 0.030 - 0.061: 230 0.061 - 0.091: 70 0.091 - 0.121: 40 0.121 - 0.152: 3 Chirality restraints: 989 Sorted by residual: chirality pdb=" CA ILE A 279 " pdb=" N ILE A 279 " pdb=" C ILE A 279 " pdb=" CB ILE A 279 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA VAL A 213 " pdb=" N VAL A 213 " pdb=" C VAL A 213 " pdb=" CB VAL A 213 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" C2B FAD A1101 " pdb=" C1B FAD A1101 " pdb=" C3B FAD A1101 " pdb=" O2B FAD A1101 " both_signs ideal model delta sigma weight residual False -2.53 -2.66 0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 986 not shown) Planarity restraints: 1157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 333 " 0.011 2.00e-02 2.50e+03 9.80e-03 1.68e+00 pdb=" CG PHE A 333 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 333 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 333 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 333 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 333 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 333 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 447 " -0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO A 448 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 448 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 448 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 358 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 359 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 359 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 359 " -0.017 5.00e-02 4.00e+02 ... (remaining 1154 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 684 2.75 - 3.28: 6101 3.28 - 3.82: 10540 3.82 - 4.36: 11958 4.36 - 4.90: 21249 Nonbonded interactions: 50532 Sorted by model distance: nonbonded pdb=" O VAL A 250 " pdb=" OG1 THR A 253 " model vdw 2.208 3.040 nonbonded pdb=" NE1 TRP A 732 " pdb=" OE2 GLU A 988 " model vdw 2.261 3.120 nonbonded pdb=" OH TYR A 293 " pdb=" O4 FAD A1101 " model vdw 2.265 3.040 nonbonded pdb=" OE2 GLU A 174 " pdb=" NE2 HIS A 176 " model vdw 2.324 3.120 nonbonded pdb=" OE2 GLU A 231 " pdb=" NH1 ARG A 233 " model vdw 2.328 3.120 ... (remaining 50527 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.780 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 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 0.076 6634 Z= 0.252 Angle : 0.531 8.174 8989 Z= 0.260 Chirality : 0.039 0.152 989 Planarity : 0.004 0.031 1157 Dihedral : 15.966 89.673 2478 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.86 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.30), residues: 805 helix: 2.85 (0.25), residues: 414 sheet: 1.31 (0.49), residues: 106 loop : 0.21 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 423 HIS 0.010 0.001 HIS A 703 PHE 0.022 0.001 PHE A 333 TYR 0.007 0.001 TYR A 705 ARG 0.006 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.778 Fit side-chains REVERT: A 371 ARG cc_start: 0.8347 (ptm160) cc_final: 0.8057 (ptm-80) REVERT: A 736 TYR cc_start: 0.8161 (p90) cc_final: 0.7655 (p90) REVERT: A 737 GLU cc_start: 0.7529 (tp30) cc_final: 0.7201 (mm-30) REVERT: A 959 GLN cc_start: 0.6249 (tp-100) cc_final: 0.5720 (tp-100) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2650 time to fit residues: 37.6415 Evaluate side-chains 103 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6634 Z= 0.180 Angle : 0.467 5.869 8989 Z= 0.241 Chirality : 0.038 0.145 989 Planarity : 0.004 0.033 1157 Dihedral : 6.732 88.298 933 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.24 % Favored : 97.64 % Rotamer: Outliers : 1.18 % Allowed : 5.76 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.30), residues: 805 helix: 2.89 (0.24), residues: 425 sheet: 1.06 (0.48), residues: 105 loop : 0.11 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 423 HIS 0.002 0.001 HIS A 343 PHE 0.018 0.001 PHE A 333 TYR 0.007 0.001 TYR A 265 ARG 0.003 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.773 Fit side-chains REVERT: A 611 PHE cc_start: 0.7489 (m-80) cc_final: 0.7181 (m-80) REVERT: A 737 GLU cc_start: 0.7563 (tp30) cc_final: 0.7189 (mm-30) REVERT: A 1004 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7857 (tm-30) REVERT: A 1008 ASP cc_start: 0.7720 (m-30) cc_final: 0.6954 (m-30) outliers start: 8 outliers final: 7 residues processed: 108 average time/residue: 0.3049 time to fit residues: 41.7533 Evaluate side-chains 107 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1047 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 606 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6634 Z= 0.206 Angle : 0.461 6.184 8989 Z= 0.237 Chirality : 0.038 0.143 989 Planarity : 0.003 0.031 1157 Dihedral : 6.483 80.100 933 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % Rotamer: Outliers : 1.33 % Allowed : 7.24 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.30), residues: 805 helix: 2.93 (0.24), residues: 425 sheet: 0.98 (0.50), residues: 105 loop : -0.00 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 423 HIS 0.006 0.001 HIS A 739 PHE 0.018 0.001 PHE A 333 TYR 0.010 0.001 TYR A 736 ARG 0.003 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.788 Fit side-chains REVERT: A 1004 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7843 (tm-30) REVERT: A 1008 ASP cc_start: 0.7702 (m-30) cc_final: 0.6860 (m-30) outliers start: 9 outliers final: 8 residues processed: 105 average time/residue: 0.2494 time to fit residues: 33.0242 Evaluate side-chains 104 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1047 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 739 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6634 Z= 0.199 Angle : 0.449 6.212 8989 Z= 0.231 Chirality : 0.038 0.144 989 Planarity : 0.003 0.030 1157 Dihedral : 6.308 73.548 933 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.11 % Favored : 97.76 % Rotamer: Outliers : 1.48 % Allowed : 8.42 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.30), residues: 805 helix: 3.01 (0.24), residues: 425 sheet: 1.08 (0.52), residues: 95 loop : -0.02 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 423 HIS 0.002 0.001 HIS A 343 PHE 0.017 0.001 PHE A 333 TYR 0.009 0.001 TYR A 736 ARG 0.004 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.693 Fit side-chains REVERT: A 254 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: A 1004 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 1008 ASP cc_start: 0.7729 (m-30) cc_final: 0.6852 (m-30) outliers start: 10 outliers final: 7 residues processed: 106 average time/residue: 0.2940 time to fit residues: 39.5228 Evaluate side-chains 107 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1047 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.0470 chunk 70 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 725 HIS A 739 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 6634 Z= 0.374 Angle : 0.541 7.204 8989 Z= 0.278 Chirality : 0.041 0.151 989 Planarity : 0.004 0.031 1157 Dihedral : 6.444 62.565 933 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.48 % Favored : 97.39 % Rotamer: Outliers : 2.22 % Allowed : 8.27 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.30), residues: 805 helix: 2.70 (0.24), residues: 426 sheet: 0.97 (0.52), residues: 97 loop : -0.18 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 423 HIS 0.008 0.001 HIS A 739 PHE 0.022 0.002 PHE A 333 TYR 0.008 0.001 TYR A 483 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: A 737 GLU cc_start: 0.7593 (tp30) cc_final: 0.7122 (mm-30) REVERT: A 1008 ASP cc_start: 0.7696 (m-30) cc_final: 0.7128 (m-30) outliers start: 15 outliers final: 9 residues processed: 108 average time/residue: 0.2715 time to fit residues: 36.5854 Evaluate side-chains 109 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1047 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 44 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6634 Z= 0.168 Angle : 0.449 6.429 8989 Z= 0.232 Chirality : 0.037 0.145 989 Planarity : 0.003 0.030 1157 Dihedral : 6.080 50.315 933 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % Rotamer: Outliers : 1.62 % Allowed : 9.90 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.30), residues: 805 helix: 2.94 (0.24), residues: 426 sheet: 1.02 (0.53), residues: 95 loop : -0.08 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 423 HIS 0.008 0.001 HIS A 739 PHE 0.019 0.001 PHE A 333 TYR 0.007 0.001 TYR A 736 ARG 0.003 0.000 ARG A 924 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7286 (mp10) REVERT: A 550 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7623 (mm) REVERT: A 737 GLU cc_start: 0.7636 (tp30) cc_final: 0.7116 (mm-30) REVERT: A 1004 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 1008 ASP cc_start: 0.7761 (m-30) cc_final: 0.6948 (m-30) outliers start: 11 outliers final: 7 residues processed: 113 average time/residue: 0.2632 time to fit residues: 37.2058 Evaluate side-chains 111 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1047 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.0010 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 HIS A 739 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6634 Z= 0.227 Angle : 0.474 6.572 8989 Z= 0.243 Chirality : 0.038 0.145 989 Planarity : 0.004 0.029 1157 Dihedral : 6.149 48.994 933 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.86 % Favored : 98.01 % Rotamer: Outliers : 1.92 % Allowed : 9.90 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.30), residues: 805 helix: 2.91 (0.24), residues: 426 sheet: 0.94 (0.52), residues: 97 loop : -0.12 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 732 HIS 0.006 0.001 HIS A 739 PHE 0.021 0.001 PHE A 333 TYR 0.007 0.001 TYR A 265 ARG 0.005 0.000 ARG A 957 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: A 550 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7634 (mm) REVERT: A 737 GLU cc_start: 0.7664 (tp30) cc_final: 0.7112 (mm-30) REVERT: A 1004 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7774 (tm-30) REVERT: A 1008 ASP cc_start: 0.7743 (m-30) cc_final: 0.6934 (m-30) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.2778 time to fit residues: 38.2569 Evaluate side-chains 112 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1047 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 HIS A 725 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6634 Z= 0.192 Angle : 0.467 6.858 8989 Z= 0.238 Chirality : 0.038 0.148 989 Planarity : 0.003 0.028 1157 Dihedral : 6.102 49.163 933 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.11 % Favored : 97.76 % Rotamer: Outliers : 1.92 % Allowed : 10.78 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.30), residues: 805 helix: 2.94 (0.24), residues: 426 sheet: 0.94 (0.52), residues: 97 loop : -0.10 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 732 HIS 0.003 0.001 HIS A 718 PHE 0.021 0.001 PHE A 333 TYR 0.007 0.001 TYR A 265 ARG 0.005 0.000 ARG A 957 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: A 550 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7627 (mm) REVERT: A 737 GLU cc_start: 0.7676 (tp30) cc_final: 0.7111 (mm-30) REVERT: A 1004 GLN cc_start: 0.8340 (tm-30) cc_final: 0.7786 (tm-30) REVERT: A 1008 ASP cc_start: 0.7709 (m-30) cc_final: 0.6874 (m-30) outliers start: 13 outliers final: 9 residues processed: 110 average time/residue: 0.2540 time to fit residues: 35.2418 Evaluate side-chains 112 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1047 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6634 Z= 0.164 Angle : 0.454 6.601 8989 Z= 0.232 Chirality : 0.037 0.147 989 Planarity : 0.003 0.029 1157 Dihedral : 5.949 49.363 933 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.61 % Favored : 98.26 % Rotamer: Outliers : 1.62 % Allowed : 10.78 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.30), residues: 805 helix: 3.00 (0.24), residues: 427 sheet: 0.96 (0.52), residues: 97 loop : -0.04 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 732 HIS 0.003 0.000 HIS A 718 PHE 0.021 0.001 PHE A 333 TYR 0.007 0.001 TYR A 736 ARG 0.005 0.000 ARG A 957 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7250 (mp10) REVERT: A 550 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7612 (mm) REVERT: A 1004 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7765 (tm-30) REVERT: A 1008 ASP cc_start: 0.7680 (m-30) cc_final: 0.6830 (m-30) outliers start: 11 outliers final: 9 residues processed: 114 average time/residue: 0.2445 time to fit residues: 35.2938 Evaluate side-chains 113 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1047 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 HIS A 725 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6634 Z= 0.180 Angle : 0.464 6.702 8989 Z= 0.236 Chirality : 0.038 0.165 989 Planarity : 0.003 0.028 1157 Dihedral : 5.981 50.067 933 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.86 % Favored : 98.01 % Rotamer: Outliers : 1.77 % Allowed : 11.23 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.30), residues: 805 helix: 2.99 (0.24), residues: 427 sheet: 0.97 (0.52), residues: 97 loop : -0.03 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 732 HIS 0.002 0.001 HIS A 718 PHE 0.022 0.001 PHE A 333 TYR 0.007 0.001 TYR A 736 ARG 0.004 0.000 ARG A 957 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7238 (mp10) REVERT: A 550 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7617 (mm) REVERT: A 1004 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 1008 ASP cc_start: 0.7635 (m-30) cc_final: 0.6815 (m-30) outliers start: 12 outliers final: 9 residues processed: 110 average time/residue: 0.2515 time to fit residues: 34.8134 Evaluate side-chains 113 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1047 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 46 optimal weight: 0.0570 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 0.0040 overall best weight: 0.2468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.141432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.097441 restraints weight = 8800.063| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.41 r_work: 0.2909 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6634 Z= 0.132 Angle : 0.441 6.501 8989 Z= 0.223 Chirality : 0.037 0.145 989 Planarity : 0.003 0.029 1157 Dihedral : 5.698 47.250 933 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.61 % Favored : 98.26 % Rotamer: Outliers : 1.48 % Allowed : 11.52 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.30), residues: 805 helix: 3.11 (0.24), residues: 427 sheet: 0.98 (0.52), residues: 97 loop : 0.04 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 732 HIS 0.002 0.000 HIS A 718 PHE 0.020 0.001 PHE A 333 TYR 0.008 0.001 TYR A 736 ARG 0.006 0.000 ARG A 957 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1934.81 seconds wall clock time: 36 minutes 0.80 seconds (2160.80 seconds total)