Starting phenix.real_space_refine on Fri Dec 27 08:59:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t3n_25665/12_2024/7t3n_25665.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3n_25665/12_2024/7t3n_25665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t3n_25665/12_2024/7t3n_25665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3n_25665/12_2024/7t3n_25665.map" model { file = "/net/cci-nas-00/data/ceres_data/7t3n_25665/12_2024/7t3n_25665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3n_25665/12_2024/7t3n_25665.cif" } resolution = 3.0 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= 1.000 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 25 5.16 5 C 2318 2.51 5 N 564 2.21 5 O 605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3512 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3435 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 19, 'TRANS': 432} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 7, 'P1L:plan-1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 452, 3435 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 19, 'TRANS': 432} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 7, 'P1L:plan-1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 3526 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'I7Y': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 5.09, per 1000 atoms: 1.45 Number of scatterers: 3512 At special positions: 0 Unit cell: (75.985, 72.645, 76.82, 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 25 16.00 O 605 8.00 N 564 7.00 C 2318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 887.6 milliseconds 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 816 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 68 through 88 removed outlier: 3.745A pdb=" N ALA A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 99 removed outlier: 3.664A pdb=" N VAL A 93 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.821A pdb=" N GLY A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 136 " --> pdb=" O PHE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 150 through 167 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.879A pdb=" N ARG A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.836A pdb=" N VAL A 183 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.598A pdb=" N HIS A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 210 through 230 removed outlier: 3.565A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 227 " --> pdb=" O TYR A 223 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 264 removed outlier: 4.468A pdb=" N VAL A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N PHE A 246 " --> pdb=" O TRP A 242 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 262 " --> pdb=" O MET A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.697A pdb=" N HIS A 271 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 309 through 332 removed outlier: 4.289A pdb=" N ILE A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 325 " --> pdb=" O CYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 341 removed outlier: 3.727A pdb=" N TYR A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 353 through 376 Proline residue: A 364 - end of helix removed outlier: 3.502A pdb=" N LYS A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 405 removed outlier: 3.526A pdb=" N ARG A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 423 Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.844A pdb=" N ILE A 427 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 441 through 468 removed outlier: 3.579A pdb=" N LEU A 455 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Proline residue: A 461 - end of helix removed outlier: 3.553A pdb=" N THR A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 497 removed outlier: 3.780A pdb=" N TYR A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 507 removed outlier: 4.186A pdb=" N ASP A 507 " --> pdb=" O PRO A 504 " (cutoff:3.500A) 210 hydrogen bonds defined for protein. 615 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: 0.92 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1049 1.34 - 1.46: 744 1.46 - 1.57: 1774 1.57 - 1.69: 6 1.69 - 1.81: 44 Bond restraints: 3617 Sorted by residual: bond pdb=" C13 I7Y A 602 " pdb=" C14 I7Y A 602 " ideal model delta sigma weight residual 1.331 1.726 -0.395 2.00e-02 2.50e+03 3.90e+02 bond pdb=" C04 I7Y A 602 " pdb=" C05 I7Y A 602 " ideal model delta sigma weight residual 1.531 1.737 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C03 I7Y A 602 " pdb=" C04 I7Y A 602 " ideal model delta sigma weight residual 1.550 1.370 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" C08 I7Y A 602 " pdb=" C11 I7Y A 602 " ideal model delta sigma weight residual 1.549 1.704 -0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" C09 I7Y A 602 " pdb=" C10 I7Y A 602 " ideal model delta sigma weight residual 1.530 1.678 -0.148 2.00e-02 2.50e+03 5.45e+01 ... (remaining 3612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 4818 2.20 - 4.39: 90 4.39 - 6.59: 18 6.59 - 8.78: 8 8.78 - 10.98: 2 Bond angle restraints: 4936 Sorted by residual: angle pdb=" C11 I7Y A 602 " pdb=" C13 I7Y A 602 " pdb=" C16 I7Y A 602 " ideal model delta sigma weight residual 114.73 125.71 -10.98 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C2C I7Y A 602 " pdb=" C1C I7Y A 602 " pdb=" O5C I7Y A 602 " ideal model delta sigma weight residual 108.21 117.29 -9.08 3.00e+00 1.11e-01 9.17e+00 angle pdb=" C11 I7Y A 602 " pdb=" C13 I7Y A 602 " pdb=" C14 I7Y A 602 " ideal model delta sigma weight residual 123.36 114.97 8.39 3.00e+00 1.11e-01 7.82e+00 angle pdb=" C4C I7Y A 602 " pdb=" O11 I7Y A 602 " pdb=" CF1 I7Y A 602 " ideal model delta sigma weight residual 118.25 110.09 8.16 3.00e+00 1.11e-01 7.40e+00 angle pdb=" C1C I7Y A 602 " pdb=" C2C I7Y A 602 " pdb=" C3C I7Y A 602 " ideal model delta sigma weight residual 108.76 116.83 -8.07 3.00e+00 1.11e-01 7.24e+00 ... (remaining 4931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 1961 17.00 - 34.00: 181 34.00 - 51.00: 36 51.00 - 68.00: 7 68.00 - 85.01: 6 Dihedral angle restraints: 2191 sinusoidal: 902 harmonic: 1289 Sorted by residual: dihedral pdb=" CA LEU A 232 " pdb=" C LEU A 232 " pdb=" N ALA A 233 " pdb=" CA ALA A 233 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA THR A 240 " pdb=" C THR A 240 " pdb=" N GLY A 241 " pdb=" CA GLY A 241 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA PHE A 307 " pdb=" C PHE A 307 " pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 2188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 554 0.134 - 0.267: 8 0.267 - 0.401: 1 0.401 - 0.535: 0 0.535 - 0.668: 1 Chirality restraints: 564 Sorted by residual: chirality pdb=" C02 I7Y A 602 " pdb=" C03 I7Y A 602 " pdb=" C06 I7Y A 602 " pdb=" C10 I7Y A 602 " both_signs ideal model delta sigma weight residual False 2.93 2.26 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C04 I7Y A 602 " pdb=" C03 I7Y A 602 " pdb=" C05 I7Y A 602 " pdb=" O72 I7Y A 602 " both_signs ideal model delta sigma weight residual False 2.64 2.98 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C51 I7Y A 602 " pdb=" C41 I7Y A 602 " pdb=" C61 I7Y A 602 " pdb=" O51 I7Y A 602 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 561 not shown) Planarity restraints: 599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 I7Y A 602 " -0.067 2.00e-02 2.50e+03 2.05e-01 5.23e+02 pdb=" C13 I7Y A 602 " -0.002 2.00e-02 2.50e+03 pdb=" C14 I7Y A 602 " -0.340 2.00e-02 2.50e+03 pdb=" C15 I7Y A 602 " 0.257 2.00e-02 2.50e+03 pdb=" C16 I7Y A 602 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 230 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 231 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 310 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.23e+00 pdb=" N PRO A 311 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " -0.025 5.00e-02 4.00e+02 ... (remaining 596 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 53 2.69 - 3.24: 3551 3.24 - 3.79: 5387 3.79 - 4.35: 7467 4.35 - 4.90: 12477 Nonbonded interactions: 28935 Sorted by model distance: nonbonded pdb=" OG1 THR A 162 " pdb=" OE1 GLN A 187 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR A 327 " pdb=" OZ1 C5B A 601 " model vdw 2.241 3.040 nonbonded pdb=" O SER A 332 " pdb=" OG SER A 332 " model vdw 2.244 3.040 nonbonded pdb=" O PHE A 307 " pdb=" OH TYR A 313 " model vdw 2.348 3.040 nonbonded pdb=" N ARG A 213 " pdb=" OD2 ASP A 371 " model vdw 2.359 3.120 ... (remaining 28930 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.160 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:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.012 0.395 3617 Z= 0.793 Angle : 0.821 10.978 4936 Z= 0.383 Chirality : 0.060 0.668 564 Planarity : 0.010 0.205 599 Dihedral : 14.514 85.005 1375 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -3.24 (0.34), residues: 448 helix: -1.57 (0.26), residues: 320 sheet: None (None), residues: 0 loop : -3.35 (0.44), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 242 HIS 0.003 0.001 HIS A 128 PHE 0.011 0.001 PHE A 131 TYR 0.017 0.002 TYR A 195 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.402 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 1.3158 time to fit residues: 90.8132 Evaluate side-chains 51 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 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 176 HIS A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3617 Z= 0.234 Angle : 0.637 6.753 4936 Z= 0.321 Chirality : 0.043 0.147 564 Planarity : 0.006 0.055 599 Dihedral : 9.875 72.660 674 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.87 % Allowed : 11.34 % Favored : 87.79 % 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: -1.70 (0.38), residues: 448 helix: -0.49 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -2.61 (0.50), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 260 HIS 0.003 0.001 HIS A 487 PHE 0.008 0.001 PHE A 65 TYR 0.011 0.001 TYR A 327 ARG 0.010 0.001 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.378 Fit side-chains REVERT: A 204 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8908 (mttt) outliers start: 3 outliers final: 1 residues processed: 64 average time/residue: 1.3217 time to fit residues: 87.1731 Evaluate side-chains 49 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.0170 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 368 GLN A 407 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3617 Z= 0.207 Angle : 0.615 6.755 4936 Z= 0.308 Chirality : 0.042 0.147 564 Planarity : 0.005 0.053 599 Dihedral : 8.739 55.297 674 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.62 % Allowed : 11.92 % Favored : 85.47 % 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: -1.00 (0.40), residues: 448 helix: 0.01 (0.30), residues: 324 sheet: None (None), residues: 0 loop : -2.30 (0.51), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 242 HIS 0.003 0.001 HIS A 487 PHE 0.009 0.001 PHE A 430 TYR 0.009 0.001 TYR A 327 ARG 0.002 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.375 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 204 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8876 (mttt) REVERT: A 254 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6969 (mtt) outliers start: 9 outliers final: 2 residues processed: 59 average time/residue: 1.3068 time to fit residues: 79.4465 Evaluate side-chains 54 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 191 GLN A 407 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3617 Z= 0.239 Angle : 0.637 6.846 4936 Z= 0.319 Chirality : 0.043 0.144 564 Planarity : 0.005 0.052 599 Dihedral : 8.030 42.934 674 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.74 % Allowed : 14.24 % Favored : 84.01 % 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: -0.73 (0.40), residues: 448 helix: 0.20 (0.30), residues: 324 sheet: None (None), residues: 0 loop : -2.19 (0.51), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 260 HIS 0.003 0.001 HIS A 176 PHE 0.009 0.001 PHE A 131 TYR 0.009 0.001 TYR A 327 ARG 0.014 0.001 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.372 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 204 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8886 (mttt) REVERT: A 254 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7067 (mtt) outliers start: 6 outliers final: 3 residues processed: 56 average time/residue: 1.3511 time to fit residues: 77.8526 Evaluate side-chains 53 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 191 GLN A 407 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3617 Z= 0.238 Angle : 0.630 7.366 4936 Z= 0.316 Chirality : 0.043 0.144 564 Planarity : 0.005 0.048 599 Dihedral : 7.669 41.834 674 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.03 % Allowed : 15.12 % Favored : 82.85 % 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: -0.60 (0.40), residues: 448 helix: 0.29 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -2.17 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 260 HIS 0.004 0.001 HIS A 176 PHE 0.010 0.001 PHE A 131 TYR 0.009 0.001 TYR A 327 ARG 0.006 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.377 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 204 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8882 (mttt) REVERT: A 254 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7103 (mtt) outliers start: 7 outliers final: 3 residues processed: 53 average time/residue: 1.2669 time to fit residues: 69.3094 Evaluate side-chains 54 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3617 Z= 0.224 Angle : 0.636 7.583 4936 Z= 0.317 Chirality : 0.042 0.143 564 Planarity : 0.005 0.047 599 Dihedral : 7.488 40.804 674 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.16 % Allowed : 15.70 % Favored : 83.14 % 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: -0.40 (0.40), residues: 448 helix: 0.43 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -1.98 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 260 HIS 0.004 0.001 HIS A 176 PHE 0.009 0.001 PHE A 131 TYR 0.008 0.001 TYR A 327 ARG 0.013 0.001 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.380 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 254 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7077 (mtt) REVERT: A 369 ILE cc_start: 0.8623 (mt) cc_final: 0.8386 (mt) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 1.4060 time to fit residues: 78.1595 Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 368 GLN A 407 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3617 Z= 0.202 Angle : 0.632 8.124 4936 Z= 0.315 Chirality : 0.042 0.144 564 Planarity : 0.005 0.048 599 Dihedral : 7.254 42.350 674 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.45 % Allowed : 15.99 % Favored : 82.56 % 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: -0.28 (0.40), residues: 448 helix: 0.52 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -1.91 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 260 HIS 0.005 0.001 HIS A 176 PHE 0.008 0.001 PHE A 320 TYR 0.009 0.001 TYR A 327 ARG 0.013 0.001 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.370 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 254 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7127 (mtt) REVERT: A 369 ILE cc_start: 0.8612 (mt) cc_final: 0.8370 (mt) outliers start: 5 outliers final: 2 residues processed: 56 average time/residue: 1.3293 time to fit residues: 76.6549 Evaluate side-chains 54 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.0670 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 24 optimal weight: 0.0060 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3617 Z= 0.186 Angle : 0.618 8.419 4936 Z= 0.308 Chirality : 0.041 0.143 564 Planarity : 0.004 0.046 599 Dihedral : 7.066 44.405 674 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.87 % Allowed : 16.86 % 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: -0.15 (0.40), residues: 448 helix: 0.62 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -1.88 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 242 HIS 0.005 0.001 HIS A 176 PHE 0.009 0.001 PHE A 320 TYR 0.008 0.001 TYR A 327 ARG 0.004 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.379 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 254 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6853 (mtt) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 1.2932 time to fit residues: 68.0794 Evaluate side-chains 53 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.0030 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3617 Z= 0.209 Angle : 0.644 9.111 4936 Z= 0.322 Chirality : 0.042 0.141 564 Planarity : 0.005 0.053 599 Dihedral : 7.115 45.600 674 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.45 % Allowed : 16.57 % Favored : 81.98 % 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: -0.05 (0.41), residues: 448 helix: 0.66 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -1.76 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 260 HIS 0.005 0.001 HIS A 176 PHE 0.009 0.001 PHE A 320 TYR 0.008 0.001 TYR A 327 ARG 0.016 0.001 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.378 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 254 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6925 (mtt) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 1.2897 time to fit residues: 73.0967 Evaluate side-chains 53 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3617 Z= 0.278 Angle : 0.678 9.181 4936 Z= 0.342 Chirality : 0.044 0.140 564 Planarity : 0.005 0.046 599 Dihedral : 7.470 45.545 674 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.87 % Allowed : 17.73 % Favored : 81.40 % 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: -0.19 (0.40), residues: 448 helix: 0.54 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -1.74 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 260 HIS 0.006 0.001 HIS A 176 PHE 0.011 0.001 PHE A 131 TYR 0.010 0.001 TYR A 478 ARG 0.004 0.001 ARG A 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.380 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 254 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.6945 (mtt) REVERT: A 369 ILE cc_start: 0.8601 (mt) cc_final: 0.8351 (mt) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 1.3640 time to fit residues: 70.3446 Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 chunk 31 optimal weight: 0.0970 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.146255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.121706 restraints weight = 9147.456| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.85 r_work: 0.3276 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3617 Z= 0.200 Angle : 0.640 9.258 4936 Z= 0.320 Chirality : 0.042 0.144 564 Planarity : 0.004 0.045 599 Dihedral : 7.082 45.367 674 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.87 % Allowed : 17.73 % Favored : 81.40 % 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: -0.01 (0.41), residues: 448 helix: 0.67 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -1.68 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 242 HIS 0.006 0.001 HIS A 176 PHE 0.009 0.001 PHE A 320 TYR 0.010 0.001 TYR A 478 ARG 0.004 0.000 ARG A 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1893.77 seconds wall clock time: 34 minutes 44.58 seconds (2084.58 seconds total)