Starting phenix.real_space_refine on Fri Aug 22 17:38:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewy_50026/08_2025/9ewy_50026.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewy_50026/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ewy_50026/08_2025/9ewy_50026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewy_50026/08_2025/9ewy_50026.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ewy_50026/08_2025/9ewy_50026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewy_50026/08_2025/9ewy_50026.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.57, per 1000 atoms: 0.24 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: 0.46 Conformation dependent library (CDL) restraints added in 301.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.15 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: 1.03 Time building geometry restraints manager: 0.58 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: 1.860 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.620 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.590 ------------------------------------------------------------------------------- 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 6642 Z= 0.170 Angle : 0.533 8.174 8995 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG A 472 TYR 0.007 0.001 TYR A 705 PHE 0.022 0.001 PHE A 333 TRP 0.012 0.001 TRP A 423 HIS 0.010 0.001 HIS A 703 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6634) covalent geometry : angle 0.53127 ( 8989) hydrogen bonds : bond 0.13801 ( 369) hydrogen bonds : angle 4.37986 ( 1059) metal coordination : bond 0.00786 ( 8) metal coordination : angle 1.84038 ( 6) *********************** 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 : 0.205 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: 0.1053 time to fit residues: 14.8005 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 : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.8962 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.141326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.097631 restraints weight = 8685.172| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.34 r_work: 0.2911 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6642 Z= 0.150 Angle : 0.492 6.120 8995 Z= 0.254 Chirality : 0.039 0.146 989 Planarity : 0.004 0.032 1157 Dihedral : 6.875 87.670 933 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.48 % Favored : 97.39 % Rotamer: Outliers : 1.18 % Allowed : 5.47 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.30), residues: 805 helix: 2.82 (0.24), residues: 425 sheet: 1.06 (0.48), residues: 105 loop : 0.06 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 516 TYR 0.007 0.001 TYR A 265 PHE 0.019 0.001 PHE A 333 TRP 0.014 0.001 TRP A 423 HIS 0.002 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6634) covalent geometry : angle 0.49056 ( 8989) hydrogen bonds : bond 0.04911 ( 369) hydrogen bonds : angle 3.83967 ( 1059) metal coordination : bond 0.00446 ( 8) metal coordination : angle 1.68688 ( 6) *********************** 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 111 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.249 Fit side-chains REVERT: A 611 PHE cc_start: 0.7625 (m-80) cc_final: 0.7344 (m-80) REVERT: A 959 GLN cc_start: 0.6356 (tp-100) cc_final: 0.6150 (tp-100) REVERT: A 988 GLU cc_start: 0.9156 (tt0) cc_final: 0.8683 (tt0) REVERT: A 1004 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 1008 ASP cc_start: 0.7837 (m-30) cc_final: 0.7114 (m-30) outliers start: 8 outliers final: 7 residues processed: 107 average time/residue: 0.0897 time to fit residues: 12.2258 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 : 0.252 ------------------------------------------------------------------------------- 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 48 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 80 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.096691 restraints weight = 8692.270| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.32 r_work: 0.2889 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6642 Z= 0.212 Angle : 0.532 7.047 8995 Z= 0.273 Chirality : 0.040 0.146 989 Planarity : 0.004 0.034 1157 Dihedral : 6.691 76.467 933 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.48 % Favored : 97.39 % Rotamer: Outliers : 1.48 % Allowed : 7.68 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.30), residues: 805 helix: 2.63 (0.24), residues: 427 sheet: 0.80 (0.49), residues: 107 loop : -0.14 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 516 TYR 0.010 0.001 TYR A 736 PHE 0.020 0.002 PHE A 333 TRP 0.015 0.002 TRP A 423 HIS 0.009 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 6634) covalent geometry : angle 0.52985 ( 8989) hydrogen bonds : bond 0.05274 ( 369) hydrogen bonds : angle 3.83674 ( 1059) metal coordination : bond 0.00773 ( 8) metal coordination : angle 1.80499 ( 6) *********************** 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: 10 poor density : 98 time to evaluate : 0.245 Fit side-chains REVERT: A 611 PHE cc_start: 0.7569 (m-80) cc_final: 0.7127 (m-80) REVERT: A 737 GLU cc_start: 0.8242 (tp30) cc_final: 0.7778 (mm-30) REVERT: A 959 GLN cc_start: 0.6316 (tp-100) cc_final: 0.6093 (tp-100) REVERT: A 1008 ASP cc_start: 0.7848 (m-30) cc_final: 0.7345 (m-30) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.1019 time to fit residues: 13.0683 Evaluate side-chains 104 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1047 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.141129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.099611 restraints weight = 8650.930| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.26 r_work: 0.2912 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6642 Z= 0.127 Angle : 0.453 6.095 8995 Z= 0.234 Chirality : 0.037 0.143 989 Planarity : 0.003 0.030 1157 Dihedral : 6.296 67.488 933 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.24 % Favored : 97.64 % Rotamer: Outliers : 1.48 % Allowed : 8.86 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.30), residues: 805 helix: 2.87 (0.24), residues: 425 sheet: 1.04 (0.52), residues: 95 loop : -0.13 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 924 TYR 0.009 0.001 TYR A 736 PHE 0.018 0.001 PHE A 333 TRP 0.013 0.001 TRP A 423 HIS 0.002 0.001 HIS A 718 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6634) covalent geometry : angle 0.45152 ( 8989) hydrogen bonds : bond 0.04508 ( 369) hydrogen bonds : angle 3.64540 ( 1059) metal coordination : bond 0.00281 ( 8) metal coordination : angle 1.48291 ( 6) *********************** 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 114 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: A 1004 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7948 (tm-30) REVERT: A 1008 ASP cc_start: 0.7864 (m-30) cc_final: 0.7113 (m-30) outliers start: 10 outliers final: 7 residues processed: 109 average time/residue: 0.1006 time to fit residues: 13.6088 Evaluate side-chains 110 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 43 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.0000 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.141047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.097683 restraints weight = 8839.932| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.35 r_work: 0.2917 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6642 Z= 0.125 Angle : 0.456 6.314 8995 Z= 0.233 Chirality : 0.038 0.159 989 Planarity : 0.003 0.030 1157 Dihedral : 6.120 60.463 933 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % Rotamer: Outliers : 2.22 % Allowed : 8.71 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.30), residues: 805 helix: 2.90 (0.24), residues: 426 sheet: 0.96 (0.52), residues: 97 loop : -0.11 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 516 TYR 0.007 0.001 TYR A 736 PHE 0.019 0.001 PHE A 333 TRP 0.013 0.001 TRP A 732 HIS 0.002 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6634) covalent geometry : angle 0.45508 ( 8989) hydrogen bonds : bond 0.04422 ( 369) hydrogen bonds : angle 3.60940 ( 1059) metal coordination : bond 0.00315 ( 8) metal coordination : angle 1.32960 ( 6) *********************** 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 120 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7703 (mp10) REVERT: A 550 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7333 (mm) REVERT: A 702 GLU cc_start: 0.7822 (mp0) cc_final: 0.7558 (tp30) REVERT: A 737 GLU cc_start: 0.8162 (tp30) cc_final: 0.7644 (mm-30) REVERT: A 1004 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7936 (tm-30) REVERT: A 1008 ASP cc_start: 0.7842 (m-30) cc_final: 0.7057 (m-30) outliers start: 15 outliers final: 10 residues processed: 115 average time/residue: 0.0919 time to fit residues: 13.3809 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 : 0.179 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 452 HIS A 725 HIS A 739 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.093529 restraints weight = 8975.514| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.40 r_work: 0.2828 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6642 Z= 0.170 Angle : 0.488 6.541 8995 Z= 0.250 Chirality : 0.039 0.147 989 Planarity : 0.004 0.032 1157 Dihedral : 6.175 51.777 933 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.11 % Favored : 97.76 % Rotamer: Outliers : 2.36 % Allowed : 9.60 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.30), residues: 805 helix: 2.82 (0.24), residues: 426 sheet: 0.84 (0.50), residues: 107 loop : -0.20 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 516 TYR 0.006 0.001 TYR A 483 PHE 0.021 0.002 PHE A 333 TRP 0.016 0.001 TRP A 732 HIS 0.004 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6634) covalent geometry : angle 0.48647 ( 8989) hydrogen bonds : bond 0.04801 ( 369) hydrogen bonds : angle 3.68430 ( 1059) metal coordination : bond 0.00596 ( 8) metal coordination : angle 1.42505 ( 6) *********************** 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 121 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7655 (mp10) REVERT: A 550 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7295 (mm) REVERT: A 702 GLU cc_start: 0.7844 (mp0) cc_final: 0.7515 (tp30) REVERT: A 737 GLU cc_start: 0.8217 (tp30) cc_final: 0.7644 (mm-30) REVERT: A 1004 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7989 (tm-30) REVERT: A 1008 ASP cc_start: 0.7907 (m-30) cc_final: 0.7137 (m-30) outliers start: 16 outliers final: 9 residues processed: 114 average time/residue: 0.0945 time to fit residues: 13.6469 Evaluate side-chains 116 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 43 optimal weight: 0.1980 chunk 56 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 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 452 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 = 0.3608 r_free = 0.3608 target = 0.138712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.094834 restraints weight = 8876.261| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.41 r_work: 0.2867 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6642 Z= 0.119 Angle : 0.463 8.043 8995 Z= 0.234 Chirality : 0.038 0.146 989 Planarity : 0.003 0.031 1157 Dihedral : 6.063 47.746 933 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.36 % Favored : 97.52 % Rotamer: Outliers : 1.62 % Allowed : 10.04 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.30), residues: 805 helix: 2.94 (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 ARG 0.004 0.000 ARG A 957 TYR 0.007 0.001 TYR A 736 PHE 0.021 0.001 PHE A 333 TRP 0.014 0.001 TRP A 732 HIS 0.004 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6634) covalent geometry : angle 0.46160 ( 8989) hydrogen bonds : bond 0.04354 ( 369) hydrogen bonds : angle 3.58893 ( 1059) metal coordination : bond 0.00299 ( 8) metal coordination : angle 1.32571 ( 6) *********************** 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: 11 poor density : 106 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: A 702 GLU cc_start: 0.7878 (mp0) cc_final: 0.7546 (tp30) REVERT: A 737 GLU cc_start: 0.8283 (tp30) cc_final: 0.7680 (mm-30) REVERT: A 1004 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7972 (tm-30) REVERT: A 1008 ASP cc_start: 0.7891 (m-30) cc_final: 0.7110 (m-30) outliers start: 11 outliers final: 9 residues processed: 113 average time/residue: 0.1002 time to fit residues: 14.2934 Evaluate side-chains 112 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 0.0010 chunk 43 optimal weight: 0.0980 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.139146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.095133 restraints weight = 8942.210| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.42 r_work: 0.2879 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6642 Z= 0.103 Angle : 0.461 7.749 8995 Z= 0.230 Chirality : 0.037 0.148 989 Planarity : 0.003 0.030 1157 Dihedral : 5.950 47.942 933 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % Rotamer: Outliers : 1.33 % Allowed : 11.23 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.30), residues: 805 helix: 2.96 (0.24), residues: 427 sheet: 0.96 (0.52), residues: 97 loop : -0.05 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 957 TYR 0.008 0.001 TYR A 736 PHE 0.020 0.001 PHE A 333 TRP 0.013 0.001 TRP A 732 HIS 0.004 0.001 HIS A 718 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 6634) covalent geometry : angle 0.45973 ( 8989) hydrogen bonds : bond 0.04098 ( 369) hydrogen bonds : angle 3.53672 ( 1059) metal coordination : bond 0.00215 ( 8) metal coordination : angle 1.30145 ( 6) *********************** 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 114 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7569 (mp10) REVERT: A 550 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7599 (mm) REVERT: A 702 GLU cc_start: 0.7859 (mp0) cc_final: 0.7502 (tp30) REVERT: A 1004 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7953 (tm-30) REVERT: A 1008 ASP cc_start: 0.7897 (m-30) cc_final: 0.7111 (m-30) outliers start: 9 outliers final: 7 residues processed: 111 average time/residue: 0.0978 time to fit residues: 13.6255 Evaluate side-chains 113 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 952 LEU 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 80 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.137955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.093925 restraints weight = 9066.617| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.43 r_work: 0.2837 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6642 Z= 0.145 Angle : 0.494 7.445 8995 Z= 0.247 Chirality : 0.039 0.152 989 Planarity : 0.004 0.031 1157 Dihedral : 6.117 50.429 933 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.24 % Favored : 97.64 % Rotamer: Outliers : 1.92 % Allowed : 10.93 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.30), residues: 805 helix: 2.85 (0.24), residues: 427 sheet: 0.94 (0.52), residues: 97 loop : -0.11 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 957 TYR 0.007 0.001 TYR A 736 PHE 0.023 0.001 PHE A 333 TRP 0.013 0.001 TRP A 732 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6634) covalent geometry : angle 0.49235 ( 8989) hydrogen bonds : bond 0.04512 ( 369) hydrogen bonds : angle 3.59590 ( 1059) metal coordination : bond 0.00354 ( 8) metal coordination : angle 1.42427 ( 6) *********************** 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 115 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: A 550 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7640 (mm) REVERT: A 702 GLU cc_start: 0.7844 (mp0) cc_final: 0.7520 (tp30) REVERT: A 1006 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8255 (tm-30) REVERT: A 1008 ASP cc_start: 0.7872 (m-30) cc_final: 0.7325 (m-30) outliers start: 13 outliers final: 8 residues processed: 111 average time/residue: 0.0962 time to fit residues: 13.4371 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 : 0.187 ------------------------------------------------------------------------------- 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 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 78 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 6 optimal weight: 0.0370 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.096420 restraints weight = 8917.904| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.42 r_work: 0.2876 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6642 Z= 0.112 Angle : 0.480 7.472 8995 Z= 0.239 Chirality : 0.038 0.151 989 Planarity : 0.003 0.029 1157 Dihedral : 5.993 51.205 933 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.86 % Favored : 98.01 % Rotamer: Outliers : 1.62 % Allowed : 11.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.30), residues: 805 helix: 2.92 (0.24), residues: 427 sheet: 0.92 (0.52), residues: 97 loop : -0.07 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 957 TYR 0.007 0.001 TYR A 736 PHE 0.022 0.001 PHE A 333 TRP 0.013 0.001 TRP A 732 HIS 0.002 0.000 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6634) covalent geometry : angle 0.47872 ( 8989) hydrogen bonds : bond 0.04141 ( 369) hydrogen bonds : angle 3.52848 ( 1059) metal coordination : bond 0.00247 ( 8) metal coordination : angle 1.38515 ( 6) ********************** 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 116 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: A 550 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7606 (mm) REVERT: A 702 GLU cc_start: 0.7851 (mp0) cc_final: 0.7516 (tp30) REVERT: A 1004 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7984 (tm-30) REVERT: A 1006 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8274 (tm-30) REVERT: A 1008 ASP cc_start: 0.7858 (m-30) cc_final: 0.7145 (m-30) outliers start: 11 outliers final: 8 residues processed: 113 average time/residue: 0.1018 time to fit residues: 14.3127 Evaluate side-chains 114 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 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 54 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 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 725 HIS A 959 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.095581 restraints weight = 8874.200| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.41 r_work: 0.2873 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6642 Z= 0.109 Angle : 0.482 7.418 8995 Z= 0.239 Chirality : 0.038 0.147 989 Planarity : 0.003 0.028 1157 Dihedral : 5.935 51.473 933 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.86 % Favored : 98.01 % Rotamer: Outliers : 1.62 % Allowed : 11.82 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.53 (0.30), residues: 805 helix: 2.93 (0.24), residues: 427 sheet: 0.95 (0.52), residues: 97 loop : -0.05 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 957 TYR 0.007 0.001 TYR A 736 PHE 0.021 0.001 PHE A 333 TRP 0.018 0.001 TRP A 732 HIS 0.002 0.000 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6634) covalent geometry : angle 0.48142 ( 8989) hydrogen bonds : bond 0.04014 ( 369) hydrogen bonds : angle 3.48847 ( 1059) metal coordination : bond 0.00235 ( 8) metal coordination : angle 1.33362 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1888.00 seconds wall clock time: 32 minutes 48.88 seconds (1968.88 seconds total)