Starting phenix.real_space_refine on Fri Dec 27 09:07:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjh_37580/12_2024/8wjh_37580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjh_37580/12_2024/8wjh_37580.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/8wjh_37580/12_2024/8wjh_37580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjh_37580/12_2024/8wjh_37580.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjh_37580/12_2024/8wjh_37580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjh_37580/12_2024/8wjh_37580.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= 0.045 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: 5 Type Number sf(0) Gaussians S 29 5.16 5 Cl 1 4.86 5 C 2493 2.51 5 N 643 2.21 5 O 658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3824 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3823 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 26, 'TRANS': 478} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.85, per 1000 atoms: 0.75 Number of scatterers: 3824 At special positions: 0 Unit cell: (90.95, 77.04, 88.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 29 16.00 O 658 8.00 N 643 7.00 C 2493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.04 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 475.7 milliseconds 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 932 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 82.4% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 removed outlier: 3.618A pdb=" N LYS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 36 removed outlier: 3.601A pdb=" N THR A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Proline residue: A 27 - end of helix Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 140 through 164 Processing helix chain 'A' and resid 168 through 187 removed outlier: 3.522A pdb=" N MET A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 192 through 222 Processing helix chain 'A' and resid 223 through 253 removed outlier: 4.552A pdb=" N ALA A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 276 Proline residue: A 265 - end of helix removed outlier: 3.880A pdb=" N LEU A 271 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 288 through 303 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 339 through 366 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 373 through 399 Processing helix chain 'A' and resid 400 through 422 Processing helix chain 'A' and resid 426 through 456 removed outlier: 3.716A pdb=" N ALA A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 484 removed outlier: 3.556A pdb=" N GLY A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 485 through 488 Processing helix chain 'A' and resid 491 through 512 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 removed outlier: 4.036A pdb=" N ARG A 87 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU A 111 " --> pdb=" O ARG A 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 289 hydrogen bonds defined for protein. 858 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: 1.10 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1191 1.35 - 1.47: 985 1.47 - 1.60: 1692 1.60 - 1.72: 0 1.72 - 1.85: 45 Bond restraints: 3913 Sorted by residual: bond pdb=" N ARG A 473 " pdb=" CA ARG A 473 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.23e-02 6.61e+03 6.14e+00 bond pdb=" N THR A 470 " pdb=" CA THR A 470 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.23e-02 6.61e+03 5.34e+00 bond pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " ideal model delta sigma weight residual 1.808 1.743 0.065 3.30e-02 9.18e+02 3.88e+00 bond pdb=" CA LEU A 26 " pdb=" C LEU A 26 " ideal model delta sigma weight residual 1.521 1.543 -0.021 1.11e-02 8.12e+03 3.69e+00 bond pdb=" C VAL A 264 " pdb=" N PRO A 265 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.10e+00 ... (remaining 3908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 5118 2.87 - 5.75: 170 5.75 - 8.62: 29 8.62 - 11.50: 6 11.50 - 14.37: 4 Bond angle restraints: 5327 Sorted by residual: angle pdb=" C CYS A 136 " pdb=" CA CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sigma weight residual 110.42 124.79 -14.37 1.99e+00 2.53e-01 5.22e+01 angle pdb=" C VAL A 135 " pdb=" N CYS A 136 " pdb=" CA CYS A 136 " ideal model delta sigma weight residual 121.54 133.18 -11.64 1.91e+00 2.74e-01 3.71e+01 angle pdb=" N VAL A 460 " pdb=" CA VAL A 460 " pdb=" C VAL A 460 " ideal model delta sigma weight residual 113.43 107.42 6.01 1.09e+00 8.42e-01 3.04e+01 angle pdb=" C ALA A 390 " pdb=" N THR A 391 " pdb=" CA THR A 391 " ideal model delta sigma weight residual 121.14 112.79 8.35 1.75e+00 3.27e-01 2.27e+01 angle pdb=" N THR A 392 " pdb=" CA THR A 392 " pdb=" C THR A 392 " ideal model delta sigma weight residual 111.28 106.36 4.92 1.09e+00 8.42e-01 2.04e+01 ... (remaining 5322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2080 17.34 - 34.68: 149 34.68 - 52.02: 49 52.02 - 69.36: 19 69.36 - 86.70: 8 Dihedral angle restraints: 2305 sinusoidal: 864 harmonic: 1441 Sorted by residual: dihedral pdb=" CB CYS A 85 " pdb=" SG CYS A 85 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 11.55 81.45 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 113 " pdb=" CB CYS A 113 " ideal model delta sinusoidal sigma weight residual -86.00 -151.66 65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" C CYS A 136 " pdb=" N CYS A 136 " pdb=" CA CYS A 136 " pdb=" CB CYS A 136 " ideal model delta harmonic sigma weight residual -122.60 -140.65 18.05 0 2.50e+00 1.60e-01 5.21e+01 ... (remaining 2302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 578 0.116 - 0.232: 47 0.232 - 0.349: 1 0.349 - 0.465: 1 0.465 - 0.581: 2 Chirality restraints: 629 Sorted by residual: chirality pdb=" CA CYS A 136 " pdb=" N CYS A 136 " pdb=" C CYS A 136 " pdb=" CB CYS A 136 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.43e+00 chirality pdb=" CG LEU A 296 " pdb=" CB LEU A 296 " pdb=" CD1 LEU A 296 " pdb=" CD2 LEU A 296 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE A 269 " pdb=" CA ILE A 269 " pdb=" CG1 ILE A 269 " pdb=" CG2 ILE A 269 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 626 not shown) Planarity restraints: 662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 459 " -0.025 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C PRO A 459 " 0.084 2.00e-02 2.50e+03 pdb=" O PRO A 459 " -0.031 2.00e-02 2.50e+03 pdb=" N VAL A 460 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 390 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C ALA A 390 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 390 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 391 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 94 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C GLN A 94 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN A 94 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 95 " 0.014 2.00e-02 2.50e+03 ... (remaining 659 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 754 2.78 - 3.31: 3894 3.31 - 3.84: 6500 3.84 - 4.37: 7086 4.37 - 4.90: 12471 Nonbonded interactions: 30705 Sorted by model distance: nonbonded pdb=" OD1 ASP A 366 " pdb=" NH2 ARG A 486 " model vdw 2.256 3.120 nonbonded pdb=" O MET A 218 " pdb=" OG1 THR A 222 " model vdw 2.306 3.040 nonbonded pdb=" O GLN A 424 " pdb=" NE2 GLN A 427 " model vdw 2.344 3.120 nonbonded pdb=" O LEU A 212 " pdb=" OG1 THR A 216 " model vdw 2.374 3.040 nonbonded pdb=" NH2 ARG A 89 " pdb=" O ALA A 108 " model vdw 2.383 3.120 ... (remaining 30700 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: 0.270 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.530 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 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 : 0.006 0.070 3913 Z= 0.399 Angle : 1.268 14.373 5327 Z= 0.719 Chirality : 0.069 0.581 629 Planarity : 0.009 0.064 662 Dihedral : 15.606 86.704 1367 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.00 % Allowed : 19.75 % Favored : 79.25 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.35), residues: 499 helix: 0.78 (0.25), residues: 374 sheet: None (None), residues: 0 loop : -0.42 (0.55), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 282 HIS 0.003 0.001 HIS A 47 PHE 0.031 0.003 PHE A 354 TYR 0.021 0.005 TYR A 119 ARG 0.017 0.003 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.398 Fit side-chains REVERT: A 473 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6036 (mtp180) outliers start: 4 outliers final: 0 residues processed: 33 average time/residue: 0.1522 time to fit residues: 6.7433 Evaluate side-chains 30 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3913 Z= 0.229 Angle : 0.643 7.056 5327 Z= 0.328 Chirality : 0.041 0.189 629 Planarity : 0.004 0.030 662 Dihedral : 5.345 58.324 538 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.00 % Allowed : 17.00 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.78 (0.38), residues: 499 helix: 1.67 (0.27), residues: 375 sheet: -0.34 (1.52), residues: 10 loop : -0.17 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 255 HIS 0.001 0.000 HIS A 52 PHE 0.018 0.002 PHE A 267 TYR 0.011 0.002 TYR A 361 ARG 0.002 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.414 Fit side-chains REVERT: A 473 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.7003 (mtt180) outliers start: 8 outliers final: 3 residues processed: 35 average time/residue: 0.1385 time to fit residues: 6.8313 Evaluate side-chains 32 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 473 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3913 Z= 0.232 Angle : 0.614 11.301 5327 Z= 0.304 Chirality : 0.039 0.166 629 Planarity : 0.004 0.035 662 Dihedral : 4.999 52.719 538 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.75 % Allowed : 17.75 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.54 (0.38), residues: 499 helix: 1.40 (0.27), residues: 387 sheet: -0.95 (1.44), residues: 10 loop : 0.01 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 282 HIS 0.001 0.000 HIS A 305 PHE 0.016 0.002 PHE A 205 TYR 0.011 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.394 Fit side-chains REVERT: A 136 CYS cc_start: 0.6574 (OUTLIER) cc_final: 0.6371 (t) REVERT: A 411 MET cc_start: 0.6622 (mmp) cc_final: 0.6396 (tpp) REVERT: A 482 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7135 (tp) outliers start: 11 outliers final: 5 residues processed: 39 average time/residue: 0.1222 time to fit residues: 6.6295 Evaluate side-chains 34 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 482 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.0060 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 overall best weight: 0.4934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3913 Z= 0.176 Angle : 0.536 6.355 5327 Z= 0.269 Chirality : 0.038 0.165 629 Planarity : 0.004 0.036 662 Dihedral : 3.902 17.705 534 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.75 % Allowed : 18.00 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.38), residues: 499 helix: 1.46 (0.27), residues: 390 sheet: -1.23 (1.45), residues: 10 loop : 0.17 (0.65), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 282 HIS 0.001 0.000 HIS A 52 PHE 0.014 0.001 PHE A 354 TYR 0.008 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.406 Fit side-chains REVERT: A 1 MET cc_start: 0.4996 (mtm) cc_final: 0.3857 (pmm) REVERT: A 136 CYS cc_start: 0.6706 (OUTLIER) cc_final: 0.6503 (t) REVERT: A 411 MET cc_start: 0.6727 (mmp) cc_final: 0.6495 (tpp) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.1202 time to fit residues: 6.2868 Evaluate side-chains 34 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.0570 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 0.0030 chunk 28 optimal weight: 2.9990 overall best weight: 0.7710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3913 Z= 0.212 Angle : 0.551 6.597 5327 Z= 0.276 Chirality : 0.038 0.150 629 Planarity : 0.004 0.036 662 Dihedral : 3.911 16.803 534 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.25 % Allowed : 20.25 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.39), residues: 499 helix: 1.48 (0.27), residues: 384 sheet: -1.49 (1.47), residues: 10 loop : 0.45 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 52 PHE 0.014 0.001 PHE A 205 TYR 0.009 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5028 (mtm) cc_final: 0.3726 (pmm) REVERT: A 136 CYS cc_start: 0.6681 (OUTLIER) cc_final: 0.6473 (t) REVERT: A 411 MET cc_start: 0.6956 (mmp) cc_final: 0.6634 (tpp) REVERT: A 482 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7169 (tp) outliers start: 9 outliers final: 5 residues processed: 37 average time/residue: 0.1208 time to fit residues: 6.3968 Evaluate side-chains 34 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 482 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.2980 chunk 48 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3913 Z= 0.159 Angle : 0.511 6.162 5327 Z= 0.255 Chirality : 0.037 0.147 629 Planarity : 0.004 0.035 662 Dihedral : 3.815 16.536 534 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.25 % Allowed : 20.75 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.39), residues: 499 helix: 1.57 (0.27), residues: 388 sheet: -1.64 (1.45), residues: 10 loop : 0.63 (0.70), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 282 HIS 0.001 0.000 HIS A 47 PHE 0.013 0.001 PHE A 354 TYR 0.009 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4894 (mtm) cc_final: 0.3757 (pmm) REVERT: A 120 ASP cc_start: 0.7720 (m-30) cc_final: 0.6808 (p0) REVERT: A 231 MET cc_start: 0.7185 (mmp) cc_final: 0.6872 (mmp) REVERT: A 317 MET cc_start: 0.5063 (pmm) cc_final: 0.4559 (ppp) REVERT: A 411 MET cc_start: 0.6934 (mmp) cc_final: 0.6634 (tpp) REVERT: A 482 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.7078 (tp) outliers start: 9 outliers final: 4 residues processed: 37 average time/residue: 0.1175 time to fit residues: 6.2563 Evaluate side-chains 31 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 482 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3913 Z= 0.213 Angle : 0.547 6.177 5327 Z= 0.272 Chirality : 0.038 0.138 629 Planarity : 0.004 0.035 662 Dihedral : 3.828 15.241 534 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.25 % Allowed : 21.75 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.82 (0.39), residues: 499 helix: 1.48 (0.27), residues: 388 sheet: None (None), residues: 0 loop : 0.48 (0.66), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 305 PHE 0.012 0.001 PHE A 205 TYR 0.008 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4971 (mtm) cc_final: 0.3729 (pmm) REVERT: A 24 PHE cc_start: 0.7853 (m-80) cc_final: 0.7428 (m-80) REVERT: A 120 ASP cc_start: 0.7734 (m-30) cc_final: 0.6846 (p0) REVERT: A 317 MET cc_start: 0.5285 (pmm) cc_final: 0.4733 (ppp) REVERT: A 411 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6636 (tpp) REVERT: A 419 ASN cc_start: 0.8150 (t0) cc_final: 0.7854 (t0) outliers start: 9 outliers final: 6 residues processed: 40 average time/residue: 0.1043 time to fit residues: 6.2168 Evaluate side-chains 39 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 411 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3913 Z= 0.178 Angle : 0.520 6.067 5327 Z= 0.259 Chirality : 0.037 0.137 629 Planarity : 0.004 0.035 662 Dihedral : 3.792 15.670 534 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.25 % Allowed : 22.25 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.88 (0.39), residues: 499 helix: 1.54 (0.27), residues: 388 sheet: None (None), residues: 0 loop : 0.45 (0.67), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.001 0.000 HIS A 47 PHE 0.012 0.001 PHE A 354 TYR 0.009 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4964 (mtm) cc_final: 0.3773 (pmm) REVERT: A 120 ASP cc_start: 0.7714 (m-30) cc_final: 0.6831 (p0) REVERT: A 231 MET cc_start: 0.7015 (mmp) cc_final: 0.6610 (mmp) REVERT: A 317 MET cc_start: 0.5329 (pmm) cc_final: 0.4801 (ppp) REVERT: A 411 MET cc_start: 0.6959 (mmp) cc_final: 0.6625 (tpp) REVERT: A 473 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7148 (mtt180) REVERT: A 482 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.7073 (tp) outliers start: 9 outliers final: 6 residues processed: 37 average time/residue: 0.1260 time to fit residues: 6.4862 Evaluate side-chains 36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 482 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3913 Z= 0.210 Angle : 0.541 6.147 5327 Z= 0.269 Chirality : 0.038 0.128 629 Planarity : 0.004 0.036 662 Dihedral : 3.804 14.632 534 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.25 % Allowed : 21.75 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.39), residues: 499 helix: 1.67 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.15 (0.63), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 47 PHE 0.012 0.001 PHE A 205 TYR 0.008 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4987 (mtm) cc_final: 0.3749 (pmm) REVERT: A 28 CYS cc_start: 0.7910 (m) cc_final: 0.7603 (p) REVERT: A 120 ASP cc_start: 0.7710 (m-30) cc_final: 0.6794 (p0) REVERT: A 317 MET cc_start: 0.5440 (pmm) cc_final: 0.4958 (ppp) REVERT: A 411 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6659 (tpp) REVERT: A 473 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7162 (mtt180) outliers start: 9 outliers final: 6 residues processed: 35 average time/residue: 0.1323 time to fit residues: 6.5594 Evaluate side-chains 35 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 473 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3913 Z= 0.266 Angle : 0.581 6.744 5327 Z= 0.289 Chirality : 0.039 0.129 629 Planarity : 0.004 0.036 662 Dihedral : 3.957 15.393 534 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.25 % Allowed : 21.75 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.39), residues: 499 helix: 1.63 (0.27), residues: 366 sheet: None (None), residues: 0 loop : 0.16 (0.60), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 275 HIS 0.001 0.000 HIS A 47 PHE 0.014 0.001 PHE A 205 TYR 0.009 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5124 (mtm) cc_final: 0.3801 (pmm) REVERT: A 24 PHE cc_start: 0.7829 (m-80) cc_final: 0.7469 (m-80) REVERT: A 28 CYS cc_start: 0.7943 (m) cc_final: 0.7601 (p) REVERT: A 120 ASP cc_start: 0.7719 (m-30) cc_final: 0.6755 (p0) REVERT: A 317 MET cc_start: 0.5481 (pmm) cc_final: 0.5019 (ppp) REVERT: A 411 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6662 (tpp) REVERT: A 473 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7226 (mtt180) outliers start: 9 outliers final: 5 residues processed: 40 average time/residue: 0.1366 time to fit residues: 7.3721 Evaluate side-chains 38 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 473 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 7 optimal weight: 0.0010 chunk 34 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.0000 chunk 30 optimal weight: 5.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.191440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135347 restraints weight = 3729.061| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.29 r_work: 0.3282 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3913 Z= 0.166 Angle : 0.524 6.621 5327 Z= 0.260 Chirality : 0.037 0.129 629 Planarity : 0.004 0.036 662 Dihedral : 3.808 15.421 534 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.00 % Allowed : 22.00 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.01 (0.39), residues: 499 helix: 1.71 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.33 (0.63), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 175 HIS 0.001 0.000 HIS A 47 PHE 0.012 0.001 PHE A 354 TYR 0.009 0.001 TYR A 361 ARG 0.003 0.000 ARG A 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1129.22 seconds wall clock time: 21 minutes 15.78 seconds (1275.78 seconds total)