Starting phenix.real_space_refine on Tue Feb 11 08:10:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hrn_34979/02_2025/8hrn_34979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hrn_34979/02_2025/8hrn_34979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hrn_34979/02_2025/8hrn_34979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hrn_34979/02_2025/8hrn_34979.map" model { file = "/net/cci-nas-00/data/ceres_data/8hrn_34979/02_2025/8hrn_34979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hrn_34979/02_2025/8hrn_34979.cif" } resolution = 3.9 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= 0.037 sd= 0.100 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 29 5.16 5 C 3115 2.51 5 N 806 2.21 5 O 920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Time building chain proxies: 3.60, per 1000 atoms: 0.74 Number of scatterers: 4870 At special positions: 0 Unit cell: (84.0942, 85.1324, 71.6358, 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 29 16.00 O 920 8.00 N 806 7.00 C 3115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 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: 1.16 Conformation dependent library (CDL) restraints added in 552.9 milliseconds 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 65.5% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.588A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.779A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.921A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.569A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.747A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.560A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.964A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.567A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.887A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.756A pdb=" N MET A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 299 removed outlier: 4.227A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.954A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.003A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.792A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.718A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.648A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.208A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 474 through 482 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.686A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.896A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.611A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.389A pdb=" N VAL A 132 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 142 " --> pdb=" O VAL A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.452A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.500A pdb=" N ALA A 348 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 359 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASP A 350 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ARG A 357 " --> pdb=" O ASP A 350 " (cutoff:3.500A) 225 hydrogen bonds defined for protein. 645 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: 1.26 Time building geometry restraints manager: 1.36 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: 1575 1.34 - 1.46: 1252 1.46 - 1.58: 2129 1.58 - 1.70: 1 1.70 - 1.82: 50 Bond restraints: 5007 Sorted by residual: bond pdb=" CB PRO A 565 " pdb=" CG PRO A 565 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.06e+01 bond pdb=" CG PRO A 565 " pdb=" CD PRO A 565 " ideal model delta sigma weight residual 1.503 1.412 0.091 3.40e-02 8.65e+02 7.12e+00 bond pdb=" N PRO A 565 " pdb=" CD PRO A 565 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 5.88e+00 bond pdb=" N PRO A 565 " pdb=" CA PRO A 565 " ideal model delta sigma weight residual 1.465 1.442 0.023 1.10e-02 8.26e+03 4.23e+00 bond pdb=" CG LEU A 595 " pdb=" CD1 LEU A 595 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.59e+00 ... (remaining 5002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 6728 3.36 - 6.73: 66 6.73 - 10.09: 8 10.09 - 13.46: 0 13.46 - 16.82: 1 Bond angle restraints: 6803 Sorted by residual: angle pdb=" CA PRO A 565 " pdb=" N PRO A 565 " pdb=" CD PRO A 565 " ideal model delta sigma weight residual 112.00 95.18 16.82 1.40e+00 5.10e-01 1.44e+02 angle pdb=" N PRO A 565 " pdb=" CD PRO A 565 " pdb=" CG PRO A 565 " ideal model delta sigma weight residual 103.20 95.37 7.83 1.50e+00 4.44e-01 2.72e+01 angle pdb=" C LEU A 267 " pdb=" N GLY A 268 " pdb=" CA GLY A 268 " ideal model delta sigma weight residual 123.30 119.20 4.10 1.06e+00 8.90e-01 1.49e+01 angle pdb=" CB LYS A 476 " pdb=" CG LYS A 476 " pdb=" CD LYS A 476 " ideal model delta sigma weight residual 111.30 119.28 -7.98 2.30e+00 1.89e-01 1.20e+01 angle pdb=" CA PRO A 565 " pdb=" CB PRO A 565 " pdb=" CG PRO A 565 " ideal model delta sigma weight residual 104.50 98.19 6.31 1.90e+00 2.77e-01 1.10e+01 ... (remaining 6798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 2518 17.90 - 35.80: 349 35.80 - 53.70: 70 53.70 - 71.59: 17 71.59 - 89.49: 5 Dihedral angle restraints: 2959 sinusoidal: 1205 harmonic: 1754 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 49.70 43.30 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 135.56 -42.56 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" CA CYS A 530 " pdb=" C CYS A 530 " pdb=" N GLN A 531 " pdb=" CA GLN A 531 " ideal model delta harmonic sigma weight residual 180.00 160.07 19.93 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 2956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 548 0.056 - 0.112: 145 0.112 - 0.167: 13 0.167 - 0.223: 3 0.223 - 0.279: 1 Chirality restraints: 710 Sorted by residual: chirality pdb=" CB VAL A 293 " pdb=" CA VAL A 293 " pdb=" CG1 VAL A 293 " pdb=" CG2 VAL A 293 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA PRO A 565 " pdb=" N PRO A 565 " pdb=" C PRO A 565 " pdb=" CB PRO A 565 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASP A 206 " pdb=" N ASP A 206 " pdb=" C ASP A 206 " pdb=" CB ASP A 206 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 707 not shown) Planarity restraints: 881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 564 " 0.099 5.00e-02 4.00e+02 1.35e-01 2.93e+01 pdb=" N PRO A 565 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 137 " -0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO A 138 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 478 " 0.003 2.00e-02 2.50e+03 1.32e-02 4.35e+00 pdb=" CG TRP A 478 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 478 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 478 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 478 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 478 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 478 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 478 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 478 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 478 " -0.007 2.00e-02 2.50e+03 ... (remaining 878 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 89 2.64 - 3.21: 4883 3.21 - 3.77: 8361 3.77 - 4.34: 11050 4.34 - 4.90: 17182 Nonbonded interactions: 41565 Sorted by model distance: nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.080 3.040 nonbonded pdb=" NE2 GLN A 81 " pdb=" OD1 ASN A 103 " model vdw 2.150 3.120 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.151 3.040 nonbonded pdb=" O LEU A 333 " pdb=" OG1 THR A 362 " model vdw 2.176 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.198 3.120 ... (remaining 41560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.370 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.163 5007 Z= 0.295 Angle : 0.912 16.822 6803 Z= 0.532 Chirality : 0.050 0.279 710 Planarity : 0.007 0.135 881 Dihedral : 17.072 89.492 1820 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.95 % Allowed : 21.44 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.15 (0.35), residues: 595 helix: -0.62 (0.28), residues: 347 sheet: -1.41 (1.34), residues: 12 loop : -0.71 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 478 HIS 0.006 0.001 HIS A 417 PHE 0.020 0.002 PHE A 452 TYR 0.027 0.002 TYR A 385 ARG 0.005 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7403 (tmm) cc_final: 0.6907 (tmm) REVERT: A 391 LEU cc_start: 0.6794 (mt) cc_final: 0.6565 (mp) REVERT: A 476 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7146 (tppp) outliers start: 5 outliers final: 3 residues processed: 65 average time/residue: 0.1870 time to fit residues: 15.5947 Evaluate side-chains 61 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 597 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 30.0000 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.0270 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.111778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.096973 restraints weight = 18039.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.099489 restraints weight = 11052.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.101361 restraints weight = 7728.929| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5007 Z= 0.184 Angle : 0.662 10.054 6803 Z= 0.332 Chirality : 0.043 0.194 710 Planarity : 0.005 0.061 881 Dihedral : 5.190 53.414 649 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.28 % Allowed : 18.60 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.62 (0.35), residues: 595 helix: -0.21 (0.28), residues: 348 sheet: -1.51 (1.33), residues: 12 loop : -0.43 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 PHE 0.014 0.001 PHE A 525 TYR 0.011 0.001 TYR A 516 ARG 0.004 0.001 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7430 (tmm) cc_final: 0.6805 (tmm) REVERT: A 169 ARG cc_start: 0.6256 (mtt180) cc_final: 0.6002 (mtt180) REVERT: A 270 MET cc_start: 0.4445 (tpt) cc_final: 0.4221 (tpt) REVERT: A 340 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.5901 (pp30) REVERT: A 476 LYS cc_start: 0.7731 (mmmt) cc_final: 0.6789 (tppt) outliers start: 12 outliers final: 2 residues processed: 77 average time/residue: 0.1714 time to fit residues: 17.0036 Evaluate side-chains 63 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 340 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 48 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 54 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 58 optimal weight: 30.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.108695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.093323 restraints weight = 18590.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.095852 restraints weight = 11420.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.097356 restraints weight = 7964.259| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5007 Z= 0.253 Angle : 0.668 10.059 6803 Z= 0.336 Chirality : 0.044 0.130 710 Planarity : 0.005 0.047 881 Dihedral : 4.720 19.757 642 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.61 % Allowed : 19.92 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.35), residues: 595 helix: -0.24 (0.28), residues: 352 sheet: -1.31 (1.31), residues: 12 loop : -0.39 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 473 HIS 0.010 0.001 HIS A 417 PHE 0.021 0.002 PHE A 452 TYR 0.028 0.002 TYR A 237 ARG 0.004 0.001 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7685 (tmm) cc_final: 0.7039 (tmm) REVERT: A 165 TRP cc_start: 0.3561 (t60) cc_final: 0.3164 (t60) REVERT: A 171 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: A 340 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.5961 (pp30) REVERT: A 376 MET cc_start: 0.5137 (tpp) cc_final: 0.4793 (mmm) REVERT: A 579 MET cc_start: 0.8280 (tmm) cc_final: 0.8020 (ppp) outliers start: 19 outliers final: 7 residues processed: 81 average time/residue: 0.1547 time to fit residues: 16.5740 Evaluate side-chains 67 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 545 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 3 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 0.0370 chunk 36 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.108181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.092774 restraints weight = 18646.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.095216 restraints weight = 11323.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.097159 restraints weight = 7914.413| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5007 Z= 0.247 Angle : 0.664 11.219 6803 Z= 0.334 Chirality : 0.044 0.164 710 Planarity : 0.004 0.044 881 Dihedral : 4.819 17.883 642 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.04 % Allowed : 21.25 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.35), residues: 595 helix: -0.26 (0.28), residues: 349 sheet: -1.33 (1.32), residues: 12 loop : -0.32 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 477 HIS 0.011 0.001 HIS A 417 PHE 0.013 0.001 PHE A 452 TYR 0.035 0.002 TYR A 237 ARG 0.005 0.001 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8765 (t-90) cc_final: 0.8426 (t-90) REVERT: A 82 MET cc_start: 0.7731 (tmm) cc_final: 0.7039 (tmm) REVERT: A 165 TRP cc_start: 0.3308 (t60) cc_final: 0.2484 (t60) REVERT: A 340 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.5954 (pp30) REVERT: A 579 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8091 (ppp) outliers start: 16 outliers final: 9 residues processed: 75 average time/residue: 0.1620 time to fit residues: 16.1701 Evaluate side-chains 70 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 595 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 12 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.108308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.091870 restraints weight = 18073.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.094676 restraints weight = 10413.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.096865 restraints weight = 7048.175| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5007 Z= 0.200 Angle : 0.640 11.029 6803 Z= 0.318 Chirality : 0.043 0.162 710 Planarity : 0.004 0.041 881 Dihedral : 4.679 17.944 642 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.23 % Allowed : 22.20 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.53 (0.35), residues: 595 helix: -0.26 (0.28), residues: 354 sheet: -1.13 (1.31), residues: 12 loop : -0.18 (0.45), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 203 HIS 0.011 0.001 HIS A 417 PHE 0.011 0.001 PHE A 452 TYR 0.018 0.002 TYR A 237 ARG 0.005 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8841 (t-90) cc_final: 0.8587 (t-90) REVERT: A 62 MET cc_start: 0.7507 (ttp) cc_final: 0.7184 (mtm) REVERT: A 82 MET cc_start: 0.7777 (tmm) cc_final: 0.7010 (tmm) REVERT: A 169 ARG cc_start: 0.6606 (mtt180) cc_final: 0.6086 (mtt180) REVERT: A 455 MET cc_start: 0.8038 (ttt) cc_final: 0.7797 (ttm) REVERT: A 477 TRP cc_start: 0.7596 (OUTLIER) cc_final: 0.6380 (t-100) REVERT: A 579 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8188 (ppp) outliers start: 17 outliers final: 11 residues processed: 74 average time/residue: 0.1612 time to fit residues: 15.8782 Evaluate side-chains 71 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 41 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.107779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.091027 restraints weight = 18315.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.094025 restraints weight = 10662.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.096127 restraints weight = 7137.531| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5007 Z= 0.222 Angle : 0.661 11.606 6803 Z= 0.329 Chirality : 0.043 0.165 710 Planarity : 0.004 0.040 881 Dihedral : 4.651 17.854 642 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.80 % Allowed : 22.96 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.52 (0.35), residues: 595 helix: -0.22 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.29 (0.44), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 473 HIS 0.013 0.001 HIS A 417 PHE 0.012 0.001 PHE A 452 TYR 0.017 0.002 TYR A 515 ARG 0.003 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8836 (t-90) cc_final: 0.8580 (t-90) REVERT: A 82 MET cc_start: 0.7778 (tmm) cc_final: 0.6980 (tmm) REVERT: A 169 ARG cc_start: 0.6792 (mtt180) cc_final: 0.6408 (mtt-85) REVERT: A 477 TRP cc_start: 0.7591 (OUTLIER) cc_final: 0.6478 (t-100) REVERT: A 579 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8195 (ppp) outliers start: 20 outliers final: 11 residues processed: 75 average time/residue: 0.1661 time to fit residues: 16.4165 Evaluate side-chains 68 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.110112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.093624 restraints weight = 17617.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.096710 restraints weight = 10216.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.098853 restraints weight = 6786.269| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5007 Z= 0.171 Angle : 0.655 12.764 6803 Z= 0.324 Chirality : 0.044 0.277 710 Planarity : 0.005 0.099 881 Dihedral : 4.540 20.493 642 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.23 % Allowed : 24.10 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.34 (0.36), residues: 595 helix: -0.07 (0.28), residues: 351 sheet: -1.18 (1.37), residues: 12 loop : -0.16 (0.46), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 203 HIS 0.010 0.001 HIS A 417 PHE 0.010 0.001 PHE A 315 TYR 0.019 0.002 TYR A 515 ARG 0.003 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7321 (ttp) cc_final: 0.7044 (mtm) REVERT: A 82 MET cc_start: 0.7791 (tmm) cc_final: 0.7069 (tmm) REVERT: A 169 ARG cc_start: 0.6477 (mtt180) cc_final: 0.6057 (mtt180) REVERT: A 196 TYR cc_start: 0.6665 (m-10) cc_final: 0.6434 (m-10) REVERT: A 270 MET cc_start: 0.5450 (tpp) cc_final: 0.4958 (tpt) REVERT: A 477 TRP cc_start: 0.7629 (OUTLIER) cc_final: 0.6036 (t-100) REVERT: A 518 ARG cc_start: 0.8440 (ptm-80) cc_final: 0.7691 (ptm-80) REVERT: A 579 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8152 (ppp) outliers start: 17 outliers final: 9 residues processed: 77 average time/residue: 0.1697 time to fit residues: 16.8745 Evaluate side-chains 68 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.108290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.092051 restraints weight = 17349.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.094943 restraints weight = 9994.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.096917 restraints weight = 6685.274| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5007 Z= 0.223 Angle : 0.694 12.200 6803 Z= 0.341 Chirality : 0.045 0.275 710 Planarity : 0.005 0.084 881 Dihedral : 4.650 19.756 642 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.04 % Allowed : 24.86 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.32 (0.35), residues: 595 helix: -0.07 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -0.19 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.009 0.001 HIS A 417 PHE 0.009 0.001 PHE A 452 TYR 0.023 0.002 TYR A 237 ARG 0.003 0.001 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7274 (ttp) cc_final: 0.6996 (mtm) REVERT: A 82 MET cc_start: 0.7831 (tmm) cc_final: 0.7100 (tmm) REVERT: A 297 MET cc_start: 0.7952 (mpp) cc_final: 0.7746 (mpp) REVERT: A 477 TRP cc_start: 0.7679 (OUTLIER) cc_final: 0.6397 (t-100) REVERT: A 518 ARG cc_start: 0.8411 (ptm-80) cc_final: 0.7193 (ptm-80) REVERT: A 579 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8142 (ppp) outliers start: 16 outliers final: 12 residues processed: 74 average time/residue: 0.1758 time to fit residues: 16.9723 Evaluate side-chains 69 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.109670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.093174 restraints weight = 17772.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.096141 restraints weight = 10367.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.098329 restraints weight = 6957.297| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5007 Z= 0.186 Angle : 0.674 12.726 6803 Z= 0.329 Chirality : 0.043 0.168 710 Planarity : 0.005 0.077 881 Dihedral : 4.528 20.705 642 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.23 % Allowed : 25.62 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.24 (0.36), residues: 595 helix: 0.01 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -0.19 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 203 HIS 0.009 0.001 HIS A 417 PHE 0.010 0.001 PHE A 452 TYR 0.024 0.002 TYR A 237 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7321 (ttp) cc_final: 0.7044 (mtm) REVERT: A 82 MET cc_start: 0.7749 (tmm) cc_final: 0.7093 (tmm) REVERT: A 446 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7290 (mm) REVERT: A 477 TRP cc_start: 0.7627 (OUTLIER) cc_final: 0.6220 (t-100) REVERT: A 478 TRP cc_start: 0.7382 (m100) cc_final: 0.6850 (m100) REVERT: A 518 ARG cc_start: 0.8405 (ptm-80) cc_final: 0.8197 (ptm-80) REVERT: A 579 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8157 (ppp) outliers start: 17 outliers final: 10 residues processed: 71 average time/residue: 0.1744 time to fit residues: 16.3646 Evaluate side-chains 69 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.0570 chunk 34 optimal weight: 30.0000 chunk 43 optimal weight: 5.9990 overall best weight: 0.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.112299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.096031 restraints weight = 17776.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.098992 restraints weight = 10390.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.101143 restraints weight = 6960.579| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5007 Z= 0.163 Angle : 0.695 13.356 6803 Z= 0.333 Chirality : 0.043 0.183 710 Planarity : 0.004 0.064 881 Dihedral : 4.393 22.404 642 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.85 % Allowed : 26.00 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.21 (0.35), residues: 595 helix: 0.01 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -0.14 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 203 HIS 0.016 0.002 HIS A 417 PHE 0.009 0.001 PHE A 504 TYR 0.021 0.002 TYR A 237 ARG 0.003 0.000 ARG A 482 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7232 (ttp) cc_final: 0.6970 (mtm) REVERT: A 82 MET cc_start: 0.7792 (tmm) cc_final: 0.7284 (tmm) REVERT: A 169 ARG cc_start: 0.5424 (mtt-85) cc_final: 0.5216 (mtt180) REVERT: A 270 MET cc_start: 0.4274 (tpt) cc_final: 0.3849 (mmm) REVERT: A 297 MET cc_start: 0.8075 (mpp) cc_final: 0.7687 (pmm) REVERT: A 446 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7008 (mm) REVERT: A 477 TRP cc_start: 0.7597 (OUTLIER) cc_final: 0.5789 (t-100) REVERT: A 478 TRP cc_start: 0.7168 (m100) cc_final: 0.6710 (m100) REVERT: A 518 ARG cc_start: 0.8325 (ptm-80) cc_final: 0.8071 (ptm-80) REVERT: A 579 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8101 (ppp) outliers start: 15 outliers final: 11 residues processed: 79 average time/residue: 0.1690 time to fit residues: 17.3340 Evaluate side-chains 72 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 14 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.109546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.092849 restraints weight = 18329.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.095845 restraints weight = 10723.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.097940 restraints weight = 7210.182| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5007 Z= 0.222 Angle : 0.718 13.379 6803 Z= 0.350 Chirality : 0.044 0.177 710 Planarity : 0.005 0.072 881 Dihedral : 4.651 23.026 642 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.04 % Allowed : 26.38 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.18 (0.36), residues: 595 helix: 0.10 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -0.23 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 566 HIS 0.015 0.002 HIS A 417 PHE 0.021 0.002 PHE A 464 TYR 0.020 0.002 TYR A 237 ARG 0.003 0.000 ARG A 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1479.89 seconds wall clock time: 27 minutes 17.64 seconds (1637.64 seconds total)