Starting phenix.real_space_refine on Wed Jun 4 18:04:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t3n_25665/06_2025/7t3n_25665.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3n_25665/06_2025/7t3n_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_25665/06_2025/7t3n_25665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3n_25665/06_2025/7t3n_25665.map" model { file = "/net/cci-nas-00/data/ceres_data/7t3n_25665/06_2025/7t3n_25665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3n_25665/06_2025/7t3n_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-5710/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: 5.59, per 1000 atoms: 1.59 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: 1.07 Conformation dependent library (CDL) restraints added in 848.0 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: 0.40 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: 1.03 Time building geometry restraints manager: 1.24 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: 7.000 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.370 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:16.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.220 ------------------------------------------------------------------------------- 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= 0.594 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 Details of bonding type rmsd hydrogen bonds : bond 0.16221 ( 210) hydrogen bonds : angle 5.63648 ( 615) covalent geometry : bond 0.01217 ( 3617) covalent geometry : angle 0.82082 ( 4936) *********************** 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 : 0.338 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 1.2656 time to fit residues: 87.2836 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 : 0.380 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 1.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120482 restraints weight = 4793.197| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.02 r_work: 0.3263 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1170 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= 0.155 Angle : 0.637 6.898 4936 Z= 0.320 Chirality : 0.043 0.148 564 Planarity : 0.006 0.055 599 Dihedral : 9.888 73.358 674 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.87 % Allowed : 11.05 % Favored : 88.08 % 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: -1.69 (0.38), residues: 448 helix: -0.48 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -2.62 (0.50), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 260 HIS 0.003 0.001 HIS A 487 PHE 0.008 0.001 PHE A 131 TYR 0.011 0.001 TYR A 327 ARG 0.010 0.001 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 210) hydrogen bonds : angle 4.28076 ( 615) covalent geometry : bond 0.00364 ( 3617) covalent geometry : angle 0.63720 ( 4936) *********************** 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 64 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.377 Fit side-chains REVERT: A 204 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.9079 (mttt) outliers start: 3 outliers final: 1 residues processed: 62 average time/residue: 1.3483 time to fit residues: 86.0263 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 : 0.355 ------------------------------------------------------------------------------- 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 1 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.0170 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.0570 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.144655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121861 restraints weight = 5673.341| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.25 r_work: 0.3300 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3617 Z= 0.133 Angle : 0.609 6.544 4936 Z= 0.305 Chirality : 0.042 0.147 564 Planarity : 0.005 0.052 599 Dihedral : 8.547 51.729 674 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.03 % Allowed : 12.21 % Favored : 85.76 % 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: -0.92 (0.40), residues: 448 helix: 0.07 (0.30), residues: 324 sheet: None (None), residues: 0 loop : -2.27 (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 0.003 0.000 ARG A 153 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 210) hydrogen bonds : angle 4.11730 ( 615) covalent geometry : bond 0.00306 ( 3617) covalent geometry : angle 0.60935 ( 4936) *********************** 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: 7 poor density : 57 time to evaluate : 0.336 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 204 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.9068 (mttt) outliers start: 7 outliers final: 2 residues processed: 60 average time/residue: 1.2594 time to fit residues: 77.8209 Evaluate side-chains 55 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 263 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.0670 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.144696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121165 restraints weight = 6026.854| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.33 r_work: 0.3295 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1699 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= 0.136 Angle : 0.620 7.015 4936 Z= 0.309 Chirality : 0.042 0.146 564 Planarity : 0.005 0.053 599 Dihedral : 7.723 41.666 674 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.33 % Allowed : 14.24 % Favored : 83.43 % 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: -0.64 (0.40), residues: 448 helix: 0.28 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -2.17 (0.51), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 260 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 0.016 0.001 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.04436 ( 210) hydrogen bonds : angle 4.06103 ( 615) covalent geometry : bond 0.00316 ( 3617) covalent geometry : angle 0.62018 ( 4936) *********************** 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 61 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.364 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 204 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9061 (mttt) REVERT: A 254 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7863 (mpt) outliers start: 8 outliers final: 2 residues processed: 59 average time/residue: 1.2498 time to fit residues: 75.9771 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 : 0.325 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.0020 chunk 30 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.144816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120695 restraints weight = 7065.490| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.53 r_work: 0.3281 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 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 = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1775 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= 0.137 Angle : 0.613 7.317 4936 Z= 0.307 Chirality : 0.042 0.144 564 Planarity : 0.005 0.048 599 Dihedral : 7.395 40.771 674 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.74 % Allowed : 15.12 % 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: -0.45 (0.41), residues: 448 helix: 0.42 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -2.14 (0.51), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 260 HIS 0.003 0.001 HIS A 176 PHE 0.009 0.001 PHE A 430 TYR 0.008 0.001 TYR A 327 ARG 0.005 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.04422 ( 210) hydrogen bonds : angle 4.04354 ( 615) covalent geometry : bond 0.00320 ( 3617) covalent geometry : angle 0.61268 ( 4936) *********************** 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 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.382 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 254 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7654 (mpt) outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 1.3266 time to fit residues: 76.4732 Evaluate side-chains 55 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 17 optimal weight: 0.0070 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.119215 restraints weight = 9583.967| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.95 r_work: 0.3252 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3617 Z= 0.141 Angle : 0.630 7.655 4936 Z= 0.313 Chirality : 0.042 0.143 564 Planarity : 0.005 0.047 599 Dihedral : 7.354 42.303 674 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.87 % Allowed : 15.70 % Favored : 83.43 % 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: -0.30 (0.41), residues: 448 helix: 0.52 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -1.97 (0.51), residues: 127 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 0.008 0.001 PHE A 131 TYR 0.008 0.001 TYR A 327 ARG 0.013 0.001 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 210) hydrogen bonds : angle 4.06348 ( 615) covalent geometry : bond 0.00332 ( 3617) covalent geometry : angle 0.62960 ( 4936) *********************** 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: 3 poor density : 52 time to evaluate : 0.340 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 254 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7753 (mpt) REVERT: A 369 ILE cc_start: 0.8605 (mt) cc_final: 0.8370 (mt) outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 1.2433 time to fit residues: 69.2491 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 : 0.364 ------------------------------------------------------------------------------- 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 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.144825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.119541 restraints weight = 9376.403| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.92 r_work: 0.3254 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1902 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= 0.139 Angle : 0.625 7.915 4936 Z= 0.312 Chirality : 0.042 0.143 564 Planarity : 0.004 0.046 599 Dihedral : 7.267 43.637 674 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.75 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: -0.13 (0.41), residues: 448 helix: 0.61 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -1.82 (0.51), 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 0.008 0.001 PHE A 131 TYR 0.008 0.001 TYR A 327 ARG 0.005 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 210) hydrogen bonds : angle 4.03708 ( 615) covalent geometry : bond 0.00326 ( 3617) covalent geometry : angle 0.62483 ( 4936) *********************** 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 54 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.412 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 254 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7757 (mpt) outliers start: 5 outliers final: 2 residues processed: 52 average time/residue: 1.3118 time to fit residues: 70.2995 Evaluate side-chains 51 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 39 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.0980 chunk 15 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.147795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124565 restraints weight = 5657.750| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.26 r_work: 0.3343 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3617 Z= 0.122 Angle : 0.624 8.508 4936 Z= 0.310 Chirality : 0.041 0.143 564 Planarity : 0.005 0.046 599 Dihedral : 6.969 45.145 674 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.16 % Allowed : 16.57 % 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: -0.03 (0.41), residues: 448 helix: 0.70 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -1.79 (0.52), 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 0.014 0.001 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 210) hydrogen bonds : angle 3.96177 ( 615) covalent geometry : bond 0.00275 ( 3617) covalent geometry : angle 0.62401 ( 4936) *********************** 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 59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.352 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 2 residues processed: 56 average time/residue: 1.3269 time to fit residues: 76.4390 Evaluate side-chains 51 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE 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 0 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 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 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.118309 restraints weight = 9249.128| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.91 r_work: 0.3250 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3617 Z= 0.155 Angle : 0.650 8.365 4936 Z= 0.325 Chirality : 0.043 0.140 564 Planarity : 0.004 0.045 599 Dihedral : 7.238 45.860 674 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.87 % Allowed : 17.44 % Favored : 81.69 % 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: -0.06 (0.41), residues: 448 helix: 0.65 (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 0.010 0.001 PHE A 131 TYR 0.007 0.001 TYR A 327 ARG 0.004 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 210) hydrogen bonds : angle 4.05536 ( 615) covalent geometry : bond 0.00371 ( 3617) covalent geometry : angle 0.64966 ( 4936) *********************** 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 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.388 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 284 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7572 (pt0) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 1.2915 time to fit residues: 67.9723 Evaluate side-chains 51 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE 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 5 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3669 r_free = 0.3669 target = 0.143664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120897 restraints weight = 5773.571| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.23 r_work: 0.3289 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3617 Z= 0.155 Angle : 0.655 8.664 4936 Z= 0.328 Chirality : 0.043 0.141 564 Planarity : 0.004 0.045 599 Dihedral : 7.286 45.541 674 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.58 % Allowed : 17.73 % Favored : 81.69 % 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: -0.08 (0.40), residues: 448 helix: 0.62 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -1.71 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 260 HIS 0.006 0.001 HIS A 176 PHE 0.010 0.001 PHE A 131 TYR 0.007 0.001 TYR A 327 ARG 0.004 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.04635 ( 210) hydrogen bonds : angle 4.08426 ( 615) covalent geometry : bond 0.00373 ( 3617) covalent geometry : angle 0.65515 ( 4936) ********************** 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 51 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.513 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. REVERT: A 254 MET cc_start: 0.8130 (mpt) cc_final: 0.6955 (mpt) REVERT: A 284 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7552 (pt0) REVERT: A 369 ILE cc_start: 0.8639 (mt) cc_final: 0.8391 (mt) outliers start: 2 outliers final: 2 residues processed: 51 average time/residue: 1.3549 time to fit residues: 71.2583 Evaluate side-chains 51 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 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 263 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 44 optimal weight: 0.0020 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.0070 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123289 restraints weight = 7464.631| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.64 r_work: 0.3308 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3617 Z= 0.124 Angle : 0.627 9.238 4936 Z= 0.312 Chirality : 0.041 0.144 564 Planarity : 0.004 0.045 599 Dihedral : 6.931 46.363 674 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.16 % Allowed : 17.15 % Favored : 81.69 % 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: 0.07 (0.41), residues: 448 helix: 0.75 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -1.68 (0.52), residues: 127 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 0.010 0.001 PHE A 320 TYR 0.008 0.001 TYR A 327 ARG 0.004 0.001 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 210) hydrogen bonds : angle 3.98005 ( 615) covalent geometry : bond 0.00279 ( 3617) covalent geometry : angle 0.62718 ( 4936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3036.68 seconds wall clock time: 52 minutes 34.91 seconds (3154.91 seconds total)