Starting phenix.real_space_refine on Wed Mar 5 16:43:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xob_38525/03_2025/8xob_38525.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xob_38525/03_2025/8xob_38525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xob_38525/03_2025/8xob_38525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xob_38525/03_2025/8xob_38525.map" model { file = "/net/cci-nas-00/data/ceres_data/8xob_38525/03_2025/8xob_38525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xob_38525/03_2025/8xob_38525.cif" } resolution = 3.15 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= -0.002 sd= 0.092 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 1904 2.51 5 N 443 2.21 5 O 484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2858 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2858 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 2.74, per 1000 atoms: 0.96 Number of scatterers: 2858 At special positions: 0 Unit cell: (56.1, 63.75, 72.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 484 8.00 N 443 7.00 C 1904 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: 0.71 Conformation dependent library (CDL) restraints added in 360.2 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 698 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 91.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 19 through 54 removed outlier: 3.941A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 130 through 157 removed outlier: 3.530A pdb=" N LEU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 4.015A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.670A pdb=" N ILE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 270 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 323 removed outlier: 4.110A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.785A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.606A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 5.052A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 418 through 435 removed outlier: 3.810A pdb=" N ILE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 469 240 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 855 1.34 - 1.46: 549 1.46 - 1.58: 1476 1.58 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 2926 Sorted by residual: bond pdb=" N ARG A 326 " pdb=" CA ARG A 326 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 8.15e+00 bond pdb=" N SER A 325 " pdb=" CA SER A 325 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.34e-02 5.57e+03 6.77e+00 bond pdb=" N LYS A 327 " pdb=" CA LYS A 327 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.74e+00 bond pdb=" C PRO A 236 " pdb=" N PRO A 237 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.30e-02 5.92e+03 2.91e+00 bond pdb=" CA SER A 325 " pdb=" CB SER A 325 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.61e-02 3.86e+03 2.33e+00 ... (remaining 2921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 3889 2.07 - 4.13: 70 4.13 - 6.20: 21 6.20 - 8.26: 3 8.26 - 10.33: 3 Bond angle restraints: 3986 Sorted by residual: angle pdb=" N GLY A 227 " pdb=" CA GLY A 227 " pdb=" C GLY A 227 " ideal model delta sigma weight residual 113.37 119.78 -6.41 1.34e+00 5.57e-01 2.29e+01 angle pdb=" CA ARG A 326 " pdb=" C ARG A 326 " pdb=" O ARG A 326 " ideal model delta sigma weight residual 121.94 118.07 3.87 1.15e+00 7.56e-01 1.13e+01 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 116.48 -6.67 2.21e+00 2.05e-01 9.11e+00 angle pdb=" CA LEU A 228 " pdb=" CB LEU A 228 " pdb=" CG LEU A 228 " ideal model delta sigma weight residual 116.30 126.63 -10.33 3.50e+00 8.16e-02 8.71e+00 angle pdb=" CA SER A 325 " pdb=" C SER A 325 " pdb=" O SER A 325 " ideal model delta sigma weight residual 121.87 118.50 3.37 1.16e+00 7.43e-01 8.44e+00 ... (remaining 3981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 1569 17.20 - 34.40: 126 34.40 - 51.59: 14 51.59 - 68.79: 2 68.79 - 85.99: 2 Dihedral angle restraints: 1713 sinusoidal: 618 harmonic: 1095 Sorted by residual: dihedral pdb=" CA VAL A 417 " pdb=" C VAL A 417 " pdb=" N TYR A 418 " pdb=" CA TYR A 418 " ideal model delta harmonic sigma weight residual -180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA VAL A 40 " pdb=" C VAL A 40 " pdb=" N VAL A 41 " pdb=" CA VAL A 41 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA SER A 416 " pdb=" C SER A 416 " pdb=" N VAL A 417 " pdb=" CA VAL A 417 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 1710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 243 0.027 - 0.055: 149 0.055 - 0.082: 59 0.082 - 0.110: 22 0.110 - 0.137: 9 Chirality restraints: 482 Sorted by residual: chirality pdb=" CA PHE A 348 " pdb=" N PHE A 348 " pdb=" C PHE A 348 " pdb=" CB PHE A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA PRO A 159 " pdb=" N PRO A 159 " pdb=" C PRO A 159 " pdb=" CB PRO A 159 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CB VAL A 234 " pdb=" CA VAL A 234 " pdb=" CG1 VAL A 234 " pdb=" CG2 VAL A 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 479 not shown) Planarity restraints: 490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 161 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 236 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 283 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 284 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.020 5.00e-02 4.00e+02 ... (remaining 487 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 982 2.87 - 3.37: 2949 3.37 - 3.88: 4460 3.88 - 4.39: 5049 4.39 - 4.90: 8869 Nonbonded interactions: 22309 Sorted by model distance: nonbonded pdb=" O SER A 416 " pdb=" OG SER A 416 " model vdw 2.358 3.040 nonbonded pdb=" NH2 ARG A 217 " pdb=" OD2 ASP A 411 " model vdw 2.455 3.120 nonbonded pdb=" O THR A 286 " pdb=" NZ LYS A 290 " model vdw 2.530 3.120 nonbonded pdb=" OD1 ASP A 411 " pdb=" OH TYR A 418 " model vdw 2.560 3.040 nonbonded pdb=" O PRO A 473 " pdb=" CA PRO A 474 " model vdw 2.573 2.776 ... (remaining 22304 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: 1.830 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.370 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.005 0.037 2926 Z= 0.344 Angle : 0.805 10.330 3986 Z= 0.424 Chirality : 0.044 0.137 482 Planarity : 0.006 0.043 490 Dihedral : 12.866 85.990 1015 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % 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: -1.77 (0.38), residues: 383 helix: -0.64 (0.26), residues: 313 sheet: None (None), residues: 0 loop : -3.01 (0.62), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 PHE 0.016 0.002 PHE A 348 TYR 0.013 0.001 TYR A 408 ARG 0.003 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.313 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1438 time to fit residues: 7.0545 Evaluate side-chains 32 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 0.0570 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 146 ASN A 192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.166489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.134376 restraints weight = 3021.317| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.78 r_work: 0.3426 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2926 Z= 0.232 Angle : 0.701 9.986 3986 Z= 0.336 Chirality : 0.042 0.146 482 Planarity : 0.006 0.043 490 Dihedral : 4.648 18.177 405 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.00 % Allowed : 11.71 % Favored : 87.29 % 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: 0.33 (0.41), residues: 383 helix: 0.88 (0.29), residues: 301 sheet: None (None), residues: 0 loop : -2.14 (0.62), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.013 0.002 PHE A 348 TYR 0.012 0.001 TYR A 422 ARG 0.003 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.289 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.1441 time to fit residues: 6.7146 Evaluate side-chains 31 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.164223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131803 restraints weight = 3014.754| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.78 r_work: 0.3414 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2926 Z= 0.265 Angle : 0.704 9.937 3986 Z= 0.337 Chirality : 0.042 0.139 482 Planarity : 0.005 0.041 490 Dihedral : 4.562 18.146 405 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.00 % Allowed : 13.71 % Favored : 85.28 % 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: 0.82 (0.43), residues: 383 helix: 1.22 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.19 (0.67), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.014 0.002 PHE A 348 TYR 0.014 0.001 TYR A 422 ARG 0.001 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.320 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.1476 time to fit residues: 6.3297 Evaluate side-chains 33 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.164470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131966 restraints weight = 3061.815| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.80 r_work: 0.3389 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2926 Z= 0.255 Angle : 0.682 9.860 3986 Z= 0.328 Chirality : 0.042 0.139 482 Planarity : 0.005 0.041 490 Dihedral : 4.480 18.121 405 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.68 % Allowed : 14.05 % Favored : 83.28 % 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: 1.13 (0.43), residues: 383 helix: 1.45 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -2.22 (0.68), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.013 0.002 PHE A 348 TYR 0.013 0.001 TYR A 422 ARG 0.002 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.310 Fit side-chains REVERT: A 431 MET cc_start: 0.7922 (tpp) cc_final: 0.7415 (ttp) outliers start: 8 outliers final: 5 residues processed: 43 average time/residue: 0.1371 time to fit residues: 7.4582 Evaluate side-chains 38 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.0870 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.168973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137051 restraints weight = 3059.415| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.78 r_work: 0.3439 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2926 Z= 0.219 Angle : 0.669 9.785 3986 Z= 0.317 Chirality : 0.041 0.137 482 Planarity : 0.005 0.042 490 Dihedral : 4.349 17.163 405 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.01 % Allowed : 15.72 % Favored : 82.27 % 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: 1.49 (0.43), residues: 383 helix: 1.74 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.22 (0.66), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.012 0.001 PHE A 348 TYR 0.012 0.001 TYR A 422 ARG 0.001 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.331 Fit side-chains REVERT: A 431 MET cc_start: 0.7869 (tpp) cc_final: 0.7403 (ttp) outliers start: 6 outliers final: 5 residues processed: 40 average time/residue: 0.1284 time to fit residues: 6.6565 Evaluate side-chains 37 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.0170 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.166280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133438 restraints weight = 3048.220| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.84 r_work: 0.3402 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2926 Z= 0.214 Angle : 0.663 9.780 3986 Z= 0.314 Chirality : 0.041 0.135 482 Planarity : 0.005 0.042 490 Dihedral : 4.329 16.616 405 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.01 % Allowed : 17.39 % Favored : 80.60 % 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: 1.77 (0.43), residues: 383 helix: 1.91 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -2.06 (0.68), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.012 0.001 PHE A 348 TYR 0.012 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.313 Fit side-chains REVERT: A 431 MET cc_start: 0.7782 (tpp) cc_final: 0.7324 (ttp) outliers start: 6 outliers final: 5 residues processed: 38 average time/residue: 0.1305 time to fit residues: 6.3958 Evaluate side-chains 38 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.165896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133029 restraints weight = 3069.124| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.85 r_work: 0.3415 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2926 Z= 0.221 Angle : 0.663 9.765 3986 Z= 0.315 Chirality : 0.041 0.134 482 Planarity : 0.005 0.042 490 Dihedral : 4.315 16.745 405 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.67 % Allowed : 17.73 % Favored : 80.60 % 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: 1.87 (0.43), residues: 383 helix: 1.96 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -1.96 (0.68), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.012 0.001 PHE A 348 TYR 0.013 0.001 TYR A 422 ARG 0.001 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.287 Fit side-chains REVERT: A 431 MET cc_start: 0.7785 (tpp) cc_final: 0.7326 (ttp) outliers start: 5 outliers final: 5 residues processed: 38 average time/residue: 0.1298 time to fit residues: 6.3078 Evaluate side-chains 39 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 0.3980 chunk 24 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.0170 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.168436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135686 restraints weight = 2996.048| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.83 r_work: 0.3456 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2926 Z= 0.187 Angle : 0.638 9.728 3986 Z= 0.301 Chirality : 0.040 0.135 482 Planarity : 0.005 0.043 490 Dihedral : 4.215 15.485 405 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.67 % Allowed : 17.73 % Favored : 80.60 % 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: 2.22 (0.44), residues: 383 helix: 2.25 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -1.98 (0.67), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 451 HIS 0.000 0.000 HIS A 414 PHE 0.012 0.001 PHE A 348 TYR 0.010 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.312 Fit side-chains REVERT: A 431 MET cc_start: 0.7704 (tpp) cc_final: 0.7302 (ttp) outliers start: 5 outliers final: 5 residues processed: 40 average time/residue: 0.1069 time to fit residues: 5.8362 Evaluate side-chains 40 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.164363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131617 restraints weight = 3014.373| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.82 r_work: 0.3402 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2926 Z= 0.258 Angle : 0.680 9.823 3986 Z= 0.324 Chirality : 0.042 0.133 482 Planarity : 0.005 0.042 490 Dihedral : 4.322 17.203 405 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.67 % Allowed : 18.39 % Favored : 79.93 % 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: 1.87 (0.43), residues: 383 helix: 1.96 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -1.95 (0.68), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.013 0.002 PHE A 348 TYR 0.014 0.001 TYR A 422 ARG 0.001 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.308 Fit side-chains REVERT: A 431 MET cc_start: 0.7836 (tpp) cc_final: 0.7422 (ttp) outliers start: 5 outliers final: 5 residues processed: 38 average time/residue: 0.1309 time to fit residues: 6.4293 Evaluate side-chains 39 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.165181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132440 restraints weight = 2983.517| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.81 r_work: 0.3422 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2926 Z= 0.238 Angle : 0.669 9.747 3986 Z= 0.319 Chirality : 0.041 0.135 482 Planarity : 0.005 0.042 490 Dihedral : 4.327 17.311 405 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.67 % Allowed : 18.73 % Favored : 79.60 % 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: 1.92 (0.43), residues: 383 helix: 2.00 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -1.97 (0.67), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.012 0.001 PHE A 348 TYR 0.013 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.297 Fit side-chains REVERT: A 431 MET cc_start: 0.7804 (tpp) cc_final: 0.7343 (ttp) outliers start: 5 outliers final: 5 residues processed: 38 average time/residue: 0.1267 time to fit residues: 6.2425 Evaluate side-chains 39 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 28 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.166789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134016 restraints weight = 2988.294| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.83 r_work: 0.3404 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2926 Z= 0.204 Angle : 0.650 9.739 3986 Z= 0.308 Chirality : 0.041 0.134 482 Planarity : 0.005 0.042 490 Dihedral : 4.257 16.481 405 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.67 % Allowed : 18.39 % Favored : 79.93 % 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: 2.11 (0.43), residues: 383 helix: 2.17 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -2.02 (0.66), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.000 0.000 HIS A 353 PHE 0.012 0.001 PHE A 348 TYR 0.012 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1841.58 seconds wall clock time: 32 minutes 22.28 seconds (1942.28 seconds total)