Starting phenix.real_space_refine on Tue Mar 11 18:54:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewy_50026/03_2025/9ewy_50026.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewy_50026/03_2025/9ewy_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_50026/03_2025/9ewy_50026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewy_50026/03_2025/9ewy_50026.map" model { file = "/net/cci-nas-00/data/ceres_data/9ewy_50026/03_2025/9ewy_50026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewy_50026/03_2025/9ewy_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-5624/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: 4.96, per 1000 atoms: 0.76 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: 1.60 Conformation dependent library (CDL) restraints added in 947.6 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: 0.81 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: 1.95 Time building geometry restraints manager: 1.91 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: 3.430 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.580 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.750 ------------------------------------------------------------------------------- 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 : 0.693 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: 0.2543 time to fit residues: 36.0978 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 : 0.709 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.098535 restraints weight = 8536.011| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.36 r_work: 0.2915 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 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 : 0.708 Fit side-chains REVERT: A 611 PHE cc_start: 0.7503 (m-80) cc_final: 0.7173 (m-80) REVERT: A 737 GLU cc_start: 0.8170 (tp30) cc_final: 0.7623 (mm-30) REVERT: A 959 GLN cc_start: 0.6382 (tp-100) cc_final: 0.6160 (tp-100) REVERT: A 1004 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8010 (tm-30) REVERT: A 1008 ASP cc_start: 0.7861 (m-30) cc_final: 0.7150 (m-30) outliers start: 8 outliers final: 7 residues processed: 108 average time/residue: 0.2679 time to fit residues: 37.7273 Evaluate side-chains 108 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 72 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 A 959 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.099438 restraints weight = 8647.215| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.36 r_work: 0.2937 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1005 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= 0.153 Angle : 0.438 6.025 8989 Z= 0.225 Chirality : 0.037 0.142 989 Planarity : 0.003 0.032 1157 Dihedral : 6.399 81.422 933 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.86 % Favored : 98.01 % Rotamer: Outliers : 1.18 % Allowed : 7.09 % Favored : 91.73 % 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: 2.67 (0.30), residues: 805 helix: 3.01 (0.24), residues: 425 sheet: 1.03 (0.50), residues: 105 loop : 0.07 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 423 HIS 0.004 0.001 HIS A 739 PHE 0.016 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 109 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.695 Fit side-chains REVERT: A 1004 GLN cc_start: 0.8386 (tm-30) cc_final: 0.7953 (tm-30) REVERT: A 1008 ASP cc_start: 0.7841 (m-30) cc_final: 0.7048 (m-30) outliers start: 8 outliers final: 7 residues processed: 107 average time/residue: 0.2451 time to fit residues: 33.1373 Evaluate side-chains 103 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 454 ASN A 739 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.099022 restraints weight = 8675.321| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.35 r_work: 0.2929 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1140 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= 0.171 Angle : 0.434 6.137 8989 Z= 0.223 Chirality : 0.037 0.142 989 Planarity : 0.003 0.030 1157 Dihedral : 6.291 77.490 933 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % Rotamer: Outliers : 1.62 % Allowed : 7.83 % Favored : 90.55 % 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: 3.09 (0.24), residues: 425 sheet: 1.12 (0.52), residues: 95 loop : 0.03 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 732 HIS 0.002 0.000 HIS A 343 PHE 0.016 0.001 PHE A 333 TYR 0.009 0.001 TYR A 736 ARG 0.003 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 113 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.680 Fit side-chains REVERT: A 1004 GLN cc_start: 0.8406 (tm-30) cc_final: 0.7973 (tm-30) REVERT: A 1008 ASP cc_start: 0.7871 (m-30) cc_final: 0.7048 (m-30) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.2569 time to fit residues: 34.7283 Evaluate side-chains 108 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.097487 restraints weight = 8700.996| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.33 r_work: 0.2909 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6634 Z= 0.237 Angle : 0.471 6.383 8989 Z= 0.241 Chirality : 0.039 0.155 989 Planarity : 0.003 0.029 1157 Dihedral : 6.309 72.039 933 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.86 % Favored : 98.01 % Rotamer: Outliers : 1.62 % Allowed : 8.57 % Favored : 89.81 % 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: 2.57 (0.30), residues: 805 helix: 2.97 (0.24), residues: 426 sheet: 0.94 (0.50), residues: 105 loop : -0.05 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 732 HIS 0.007 0.001 HIS A 739 PHE 0.020 0.001 PHE A 333 TYR 0.006 0.001 TYR A 265 ARG 0.004 0.000 ARG A 516 *********************** 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 112 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7731 (mp10) REVERT: A 737 GLU cc_start: 0.8222 (tp30) cc_final: 0.7714 (mm-30) REVERT: A 1004 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7982 (tm-30) REVERT: A 1008 ASP cc_start: 0.7870 (m-30) cc_final: 0.7035 (m-30) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.2745 time to fit residues: 37.4767 Evaluate side-chains 109 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.098079 restraints weight = 8696.657| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.32 r_work: 0.2908 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6634 Z= 0.265 Angle : 0.487 6.525 8989 Z= 0.249 Chirality : 0.039 0.145 989 Planarity : 0.004 0.029 1157 Dihedral : 6.260 64.361 933 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.36 % Favored : 97.52 % Rotamer: Outliers : 1.77 % Allowed : 9.01 % Favored : 89.22 % 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: 2.48 (0.30), residues: 805 helix: 2.91 (0.24), residues: 426 sheet: 0.91 (0.50), residues: 105 loop : -0.12 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 423 HIS 0.006 0.001 HIS A 739 PHE 0.021 0.002 PHE A 333 TYR 0.006 0.001 TYR A 265 ARG 0.003 0.000 ARG A 516 *********************** 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 114 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7670 (mp10) REVERT: A 702 GLU cc_start: 0.7820 (mp0) cc_final: 0.7529 (tp30) REVERT: A 737 GLU cc_start: 0.8212 (tp30) cc_final: 0.7689 (mm-30) REVERT: A 1008 ASP cc_start: 0.7862 (m-30) cc_final: 0.7343 (m-30) outliers start: 12 outliers final: 8 residues processed: 108 average time/residue: 0.2513 time to fit residues: 34.1827 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 : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 69 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 0.0770 chunk 2 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.098233 restraints weight = 8749.328| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.34 r_work: 0.2928 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1320 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= 0.167 Angle : 0.450 6.485 8989 Z= 0.230 Chirality : 0.037 0.146 989 Planarity : 0.003 0.028 1157 Dihedral : 6.028 55.966 933 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.11 % Favored : 97.76 % Rotamer: Outliers : 1.48 % Allowed : 9.75 % Favored : 88.77 % 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: 1.00 (0.52), residues: 95 loop : -0.02 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 732 HIS 0.002 0.001 HIS A 718 PHE 0.020 0.001 PHE A 333 TYR 0.007 0.001 TYR A 265 ARG 0.004 0.000 ARG A 924 *********************** 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 117 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: A 550 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7638 (mm) REVERT: A 702 GLU cc_start: 0.7854 (mp0) cc_final: 0.7533 (tp30) REVERT: A 737 GLU cc_start: 0.8209 (tp30) cc_final: 0.7646 (mm-30) REVERT: A 1004 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7970 (tm-30) REVERT: A 1008 ASP cc_start: 0.7903 (m-30) cc_final: 0.7168 (m-30) outliers start: 10 outliers final: 7 residues processed: 113 average time/residue: 0.2471 time to fit residues: 35.4792 Evaluate side-chains 112 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 0.0370 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.0030 overall best weight: 0.5268 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.096158 restraints weight = 8786.781| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.39 r_work: 0.2873 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1375 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= 0.163 Angle : 0.456 7.312 8989 Z= 0.230 Chirality : 0.038 0.143 989 Planarity : 0.003 0.028 1157 Dihedral : 5.897 45.603 933 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % Rotamer: Outliers : 1.33 % Allowed : 10.49 % 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: 2.62 (0.30), residues: 805 helix: 3.01 (0.24), residues: 427 sheet: 0.95 (0.52), residues: 97 loop : 0.01 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 732 HIS 0.002 0.000 HIS A 718 PHE 0.019 0.001 PHE A 333 TYR 0.006 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 119 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: A 550 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7583 (mm) REVERT: A 702 GLU cc_start: 0.7824 (mp0) cc_final: 0.7452 (tp30) REVERT: A 737 GLU cc_start: 0.8238 (tp30) cc_final: 0.7627 (mm-30) REVERT: A 1004 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7970 (tm-30) REVERT: A 1008 ASP cc_start: 0.7834 (m-30) cc_final: 0.7098 (m-30) outliers start: 9 outliers final: 7 residues processed: 116 average time/residue: 0.2463 time to fit residues: 36.1599 Evaluate side-chains 114 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.097025 restraints weight = 8928.953| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.32 r_work: 0.2886 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6634 Z= 0.179 Angle : 0.475 7.232 8989 Z= 0.240 Chirality : 0.038 0.148 989 Planarity : 0.003 0.028 1157 Dihedral : 5.928 46.061 933 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % Rotamer: Outliers : 1.92 % Allowed : 10.19 % Favored : 87.89 % 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: 2.58 (0.30), residues: 805 helix: 2.98 (0.24), residues: 427 sheet: 0.94 (0.52), residues: 97 loop : -0.02 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 732 HIS 0.002 0.001 HIS A 126 PHE 0.021 0.001 PHE A 333 TYR 0.007 0.001 TYR A 736 ARG 0.004 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 116 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: A 550 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7617 (mm) REVERT: A 702 GLU cc_start: 0.7777 (mp0) cc_final: 0.7444 (tp30) REVERT: A 1004 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7972 (tm-30) REVERT: A 1008 ASP cc_start: 0.7837 (m-30) cc_final: 0.7082 (m-30) outliers start: 13 outliers final: 10 residues processed: 112 average time/residue: 0.2411 time to fit residues: 34.1966 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 : 0.702 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 70 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 0.0670 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.138811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.094692 restraints weight = 8995.862| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.45 r_work: 0.2867 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6634 Z= 0.195 Angle : 0.489 7.442 8989 Z= 0.246 Chirality : 0.039 0.155 989 Planarity : 0.003 0.029 1157 Dihedral : 5.988 48.059 933 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.11 % Favored : 97.76 % Rotamer: Outliers : 2.07 % Allowed : 10.19 % Favored : 87.74 % 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: 2.52 (0.30), residues: 805 helix: 2.92 (0.24), residues: 427 sheet: 0.93 (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 133 PHE 0.022 0.001 PHE A 333 TYR 0.006 0.001 TYR A 265 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 118 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: A 550 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7664 (mm) REVERT: A 702 GLU cc_start: 0.7787 (mp0) cc_final: 0.7428 (tp30) REVERT: A 1004 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 1008 ASP cc_start: 0.7873 (m-30) cc_final: 0.7088 (m-30) outliers start: 14 outliers final: 9 residues processed: 114 average time/residue: 0.2396 time to fit residues: 34.5691 Evaluate side-chains 115 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 6 optimal weight: 0.0000 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 69 optimal weight: 0.0370 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 739 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.140179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.096248 restraints weight = 9045.546| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.44 r_work: 0.2893 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6634 Z= 0.150 Angle : 0.474 7.158 8989 Z= 0.236 Chirality : 0.038 0.150 989 Planarity : 0.003 0.028 1157 Dihedral : 5.829 47.825 933 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % Rotamer: Outliers : 1.77 % Allowed : 10.49 % Favored : 87.74 % 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: 3.00 (0.24), residues: 427 sheet: 0.95 (0.52), residues: 97 loop : -0.01 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 732 HIS 0.002 0.000 HIS A 718 PHE 0.021 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: 4466.94 seconds wall clock time: 77 minutes 3.96 seconds (4623.96 seconds total)