Starting phenix.real_space_refine on Wed Jul 23 19:20:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wfj_37493/07_2025/8wfj_37493.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wfj_37493/07_2025/8wfj_37493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wfj_37493/07_2025/8wfj_37493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wfj_37493/07_2025/8wfj_37493.map" model { file = "/net/cci-nas-00/data/ceres_data/8wfj_37493/07_2025/8wfj_37493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wfj_37493/07_2025/8wfj_37493.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.154 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 34 5.16 5 C 2780 2.51 5 N 639 2.21 5 O 694 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4148 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4119 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 494} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'W5F': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.13, per 1000 atoms: 0.75 Number of scatterers: 4148 At special positions: 0 Unit cell: (81.18, 68.88, 94.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 F 1 9.00 O 694 8.00 N 639 7.00 C 2780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " distance=2.27 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: 1.05 Conformation dependent library (CDL) restraints added in 472.5 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 946 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 75.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 54 through 64 removed outlier: 3.917A pdb=" N ALA A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.923A pdb=" N VAL A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 70' Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.846A pdb=" N TYR A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 removed outlier: 4.357A pdb=" N PHE A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 96 through 110 removed outlier: 3.530A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 124 through 141 removed outlier: 4.286A pdb=" N GLY A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 155 removed outlier: 3.612A pdb=" N VAL A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 218 Processing helix chain 'A' and resid 233 through 253 removed outlier: 3.562A pdb=" N LEU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 279 Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.653A pdb=" N TYR A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.809A pdb=" N TRP A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 331 removed outlier: 3.797A pdb=" N THR A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 372 removed outlier: 3.568A pdb=" N ILE A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.534A pdb=" N ARG A 377 " --> pdb=" O ASP A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 397 removed outlier: 3.712A pdb=" N LEU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 433 removed outlier: 3.832A pdb=" N TRP A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 458 removed outlier: 3.579A pdb=" N VAL A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 465 through 495 removed outlier: 4.034A pdb=" N TRP A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE A 480 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 493 " --> pdb=" O MET A 489 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET A 494 " --> pdb=" O CYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 510 removed outlier: 3.513A pdb=" N MET A 508 " --> pdb=" O GLN A 504 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 524 removed outlier: 3.535A pdb=" N ARG A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 537 removed outlier: 3.570A pdb=" N ALA A 528 " --> pdb=" O PHE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.741A pdb=" N SER A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.755A pdb=" N LYS A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) 235 hydrogen bonds defined for protein. 690 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: 1.00 Time building geometry restraints manager: 1.25 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: 1206 1.34 - 1.46: 934 1.46 - 1.58: 2091 1.58 - 1.70: 0 1.70 - 1.81: 52 Bond restraints: 4283 Sorted by residual: bond pdb=" C14 W5F A 701 " pdb=" O02 W5F A 701 " ideal model delta sigma weight residual 1.348 1.400 -0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" C19 W5F A 701 " pdb=" C24 W5F A 701 " ideal model delta sigma weight residual 1.476 1.525 -0.049 2.00e-02 2.50e+03 5.96e+00 bond pdb=" CB ASN A 171 " pdb=" CG ASN A 171 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.70e+00 bond pdb=" C CYS A 166 " pdb=" O CYS A 166 " ideal model delta sigma weight residual 1.235 1.220 0.015 1.33e-02 5.65e+03 1.34e+00 bond pdb=" C20 W5F A 701 " pdb=" F01 W5F A 701 " ideal model delta sigma weight residual 1.344 1.365 -0.021 2.00e-02 2.50e+03 1.08e+00 ... (remaining 4278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 5690 1.49 - 2.98: 113 2.98 - 4.47: 19 4.47 - 5.95: 14 5.95 - 7.44: 5 Bond angle restraints: 5841 Sorted by residual: angle pdb=" N CYS A 175 " pdb=" CA CYS A 175 " pdb=" C CYS A 175 " ideal model delta sigma weight residual 109.40 113.89 -4.49 1.63e+00 3.76e-01 7.60e+00 angle pdb=" C21 W5F A 701 " pdb=" C10 W5F A 701 " pdb=" N05 W5F A 701 " ideal model delta sigma weight residual 116.35 108.91 7.44 3.00e+00 1.11e-01 6.15e+00 angle pdb=" CB MET A 91 " pdb=" CG MET A 91 " pdb=" SD MET A 91 " ideal model delta sigma weight residual 112.70 119.73 -7.03 3.00e+00 1.11e-01 5.49e+00 angle pdb=" C07 W5F A 701 " pdb=" O02 W5F A 701 " pdb=" C14 W5F A 701 " ideal model delta sigma weight residual 120.97 113.95 7.02 3.00e+00 1.11e-01 5.48e+00 angle pdb=" O03 W5F A 701 " pdb=" C21 W5F A 701 " pdb=" O04 W5F A 701 " ideal model delta sigma weight residual 127.09 120.08 7.01 3.00e+00 1.11e-01 5.46e+00 ... (remaining 5836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 1962 15.78 - 31.56: 299 31.56 - 47.34: 109 47.34 - 63.12: 38 63.12 - 78.90: 2 Dihedral angle restraints: 2410 sinusoidal: 916 harmonic: 1494 Sorted by residual: dihedral pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " pdb=" SG CYS A 175 " pdb=" CB CYS A 175 " ideal model delta sinusoidal sigma weight residual -86.00 -116.76 30.76 1 1.00e+01 1.00e-02 1.35e+01 dihedral pdb=" CA PHE A 524 " pdb=" C PHE A 524 " pdb=" N VAL A 525 " pdb=" CA VAL A 525 " ideal model delta harmonic sigma weight residual 180.00 -164.71 -15.29 0 5.00e+00 4.00e-02 9.35e+00 dihedral pdb=" CA ILE A 252 " pdb=" CB ILE A 252 " pdb=" CG1 ILE A 252 " pdb=" CD1 ILE A 252 " ideal model delta sinusoidal sigma weight residual 60.00 113.55 -53.55 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 2407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 458 0.038 - 0.075: 144 0.075 - 0.112: 36 0.112 - 0.150: 3 0.150 - 0.187: 1 Chirality restraints: 642 Sorted by residual: chirality pdb=" CB ILE A 399 " pdb=" CA ILE A 399 " pdb=" CG1 ILE A 399 " pdb=" CG2 ILE A 399 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA VAL A 434 " pdb=" N VAL A 434 " pdb=" C VAL A 434 " pdb=" CB VAL A 434 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CB THR A 348 " pdb=" CA THR A 348 " pdb=" OG1 THR A 348 " pdb=" CG2 THR A 348 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 639 not shown) Planarity restraints: 715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 526 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO A 527 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 209 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO A 210 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 170 " -0.008 2.00e-02 2.50e+03 6.91e-03 1.19e+00 pdb=" CG TRP A 170 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 170 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP A 170 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 170 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 170 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 170 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 170 " -0.000 2.00e-02 2.50e+03 ... (remaining 712 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1001 2.78 - 3.31: 3883 3.31 - 3.84: 6887 3.84 - 4.37: 7547 4.37 - 4.90: 13553 Nonbonded interactions: 32871 Sorted by model distance: nonbonded pdb=" OH TYR A 77 " pdb=" O VAL A 375 " model vdw 2.248 3.040 nonbonded pdb=" O PRO A 460 " pdb=" OG SER A 463 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR A 495 " pdb=" O ARG A 523 " model vdw 2.272 3.040 nonbonded pdb=" O ILE A 301 " pdb=" NE1 TRP A 307 " model vdw 2.278 3.120 nonbonded pdb=" O ASP A 309 " pdb=" OG SER A 312 " model vdw 2.286 3.040 ... (remaining 32866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.090 Find NCS groups from input model: 0.030 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 0.243 4284 Z= 0.229 Angle : 0.682 26.217 5843 Z= 0.333 Chirality : 0.039 0.187 642 Planarity : 0.004 0.053 715 Dihedral : 18.005 78.903 1461 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 30.73 % Favored : 69.27 % 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: 0.04 (0.39), residues: 512 helix: 1.11 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -2.22 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 170 HIS 0.008 0.001 HIS A 173 PHE 0.009 0.001 PHE A 408 TYR 0.014 0.001 TYR A 74 ARG 0.005 0.000 ARG A 580 Details of bonding type rmsd hydrogen bonds : bond 0.22049 ( 235) hydrogen bonds : angle 6.89387 ( 690) SS BOND : bond 0.24258 ( 1) SS BOND : angle 19.64447 ( 2) covalent geometry : bond 0.00291 ( 4283) covalent geometry : angle 0.57739 ( 5841) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.436 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1670 time to fit residues: 13.8298 Evaluate side-chains 64 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 0.0070 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.169168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.152117 restraints weight = 5607.406| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.51 r_work: 0.3551 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4284 Z= 0.149 Angle : 0.564 5.735 5843 Z= 0.292 Chirality : 0.041 0.190 642 Planarity : 0.004 0.040 715 Dihedral : 6.158 58.372 585 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 5.05 % Allowed : 27.98 % Favored : 66.97 % 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: 0.42 (0.39), residues: 512 helix: 1.48 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -2.44 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 170 HIS 0.003 0.001 HIS A 370 PHE 0.012 0.001 PHE A 109 TYR 0.016 0.001 TYR A 74 ARG 0.004 0.000 ARG A 580 Details of bonding type rmsd hydrogen bonds : bond 0.04952 ( 235) hydrogen bonds : angle 4.24056 ( 690) SS BOND : bond 0.00321 ( 1) SS BOND : angle 0.97795 ( 2) covalent geometry : bond 0.00346 ( 4283) covalent geometry : angle 0.56401 ( 5841) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.641 Fit side-chains REVERT: A 358 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.6847 (t80) outliers start: 22 outliers final: 12 residues processed: 82 average time/residue: 0.1718 time to fit residues: 19.0513 Evaluate side-chains 74 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 560 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.164567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.147645 restraints weight = 5524.581| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.47 r_work: 0.3489 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4284 Z= 0.182 Angle : 0.585 5.635 5843 Z= 0.300 Chirality : 0.042 0.203 642 Planarity : 0.004 0.043 715 Dihedral : 5.987 56.700 585 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.82 % Allowed : 29.36 % Favored : 65.83 % 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: 0.21 (0.39), residues: 512 helix: 1.32 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -2.56 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.004 0.001 HIS A 370 PHE 0.014 0.002 PHE A 408 TYR 0.020 0.002 TYR A 74 ARG 0.004 0.001 ARG A 580 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 235) hydrogen bonds : angle 3.95895 ( 690) SS BOND : bond 0.00412 ( 1) SS BOND : angle 1.37754 ( 2) covalent geometry : bond 0.00445 ( 4283) covalent geometry : angle 0.58475 ( 5841) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.429 Fit side-chains REVERT: A 231 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: A 358 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.6827 (t80) REVERT: A 590 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5849 (tp) outliers start: 21 outliers final: 12 residues processed: 78 average time/residue: 0.1509 time to fit residues: 15.7844 Evaluate side-chains 77 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 590 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.174418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.158387 restraints weight = 5669.089| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.26 r_work: 0.3654 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4284 Z= 0.124 Angle : 0.541 9.558 5843 Z= 0.273 Chirality : 0.040 0.190 642 Planarity : 0.004 0.037 715 Dihedral : 5.838 56.856 585 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.27 % Favored : 94.53 % Rotamer: Outliers : 4.82 % Allowed : 29.59 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.39), residues: 512 helix: 1.51 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -2.49 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 554 HIS 0.003 0.001 HIS A 370 PHE 0.010 0.001 PHE A 408 TYR 0.019 0.001 TYR A 497 ARG 0.004 0.000 ARG A 580 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 235) hydrogen bonds : angle 3.72513 ( 690) SS BOND : bond 0.00315 ( 1) SS BOND : angle 1.07437 ( 2) covalent geometry : bond 0.00296 ( 4283) covalent geometry : angle 0.54098 ( 5841) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.440 Fit side-chains REVERT: A 358 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.6770 (t80) outliers start: 21 outliers final: 13 residues processed: 79 average time/residue: 0.1377 time to fit residues: 14.2779 Evaluate side-chains 79 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 560 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 11 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.176342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.160362 restraints weight = 5752.723| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.24 r_work: 0.3655 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4284 Z= 0.117 Angle : 0.551 11.922 5843 Z= 0.270 Chirality : 0.040 0.190 642 Planarity : 0.004 0.040 715 Dihedral : 5.719 56.312 585 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.86 % Favored : 93.95 % Rotamer: Outliers : 5.28 % Allowed : 30.05 % Favored : 64.68 % 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: 0.52 (0.39), residues: 512 helix: 1.55 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -2.56 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 554 HIS 0.003 0.001 HIS A 370 PHE 0.010 0.001 PHE A 408 TYR 0.016 0.001 TYR A 74 ARG 0.003 0.000 ARG A 580 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 235) hydrogen bonds : angle 3.60705 ( 690) SS BOND : bond 0.00258 ( 1) SS BOND : angle 0.87685 ( 2) covalent geometry : bond 0.00277 ( 4283) covalent geometry : angle 0.55036 ( 5841) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.442 Fit side-chains REVERT: A 231 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7058 (tt0) REVERT: A 358 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.6739 (t80) REVERT: A 546 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.5801 (t80) outliers start: 23 outliers final: 15 residues processed: 83 average time/residue: 0.1456 time to fit residues: 16.0979 Evaluate side-chains 85 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 560 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.177392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.161859 restraints weight = 5667.840| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.09 r_work: 0.3681 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4284 Z= 0.113 Angle : 0.540 11.910 5843 Z= 0.265 Chirality : 0.039 0.188 642 Planarity : 0.005 0.082 715 Dihedral : 5.636 56.240 585 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.27 % Favored : 94.53 % Rotamer: Outliers : 5.96 % Allowed : 29.13 % Favored : 64.91 % 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: 0.63 (0.39), residues: 512 helix: 1.66 (0.29), residues: 350 sheet: None (None), residues: 0 loop : -2.53 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 554 HIS 0.003 0.001 HIS A 370 PHE 0.009 0.001 PHE A 408 TYR 0.015 0.001 TYR A 74 ARG 0.003 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 235) hydrogen bonds : angle 3.54557 ( 690) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.81625 ( 2) covalent geometry : bond 0.00262 ( 4283) covalent geometry : angle 0.54015 ( 5841) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.450 Fit side-chains REVERT: A 231 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: A 358 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.6867 (t80) REVERT: A 546 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.5871 (t80) outliers start: 26 outliers final: 17 residues processed: 88 average time/residue: 0.1334 time to fit residues: 15.6443 Evaluate side-chains 86 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 560 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.173574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.157808 restraints weight = 5713.158| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.21 r_work: 0.3638 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4284 Z= 0.152 Angle : 0.595 12.433 5843 Z= 0.290 Chirality : 0.041 0.195 642 Planarity : 0.005 0.075 715 Dihedral : 5.702 55.331 585 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.25 % Favored : 93.55 % Rotamer: Outliers : 5.50 % Allowed : 29.82 % Favored : 64.68 % 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: 0.42 (0.38), residues: 512 helix: 1.52 (0.29), residues: 353 sheet: None (None), residues: 0 loop : -2.73 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.004 0.001 HIS A 370 PHE 0.012 0.001 PHE A 94 TYR 0.019 0.001 TYR A 74 ARG 0.003 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 235) hydrogen bonds : angle 3.64249 ( 690) SS BOND : bond 0.00385 ( 1) SS BOND : angle 1.26015 ( 2) covalent geometry : bond 0.00374 ( 4283) covalent geometry : angle 0.59445 ( 5841) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.412 Fit side-chains REVERT: A 231 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7075 (tt0) REVERT: A 358 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.6856 (t80) REVERT: A 546 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.5891 (t80) REVERT: A 590 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.6192 (tp) outliers start: 24 outliers final: 18 residues processed: 82 average time/residue: 0.1334 time to fit residues: 14.4913 Evaluate side-chains 86 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 590 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.0470 chunk 11 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 0.0980 chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.176542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.161297 restraints weight = 5564.666| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.11 r_work: 0.3656 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4284 Z= 0.108 Angle : 0.561 12.806 5843 Z= 0.272 Chirality : 0.040 0.184 642 Planarity : 0.004 0.068 715 Dihedral : 5.629 55.725 585 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.66 % Favored : 94.14 % Rotamer: Outliers : 4.36 % Allowed : 31.42 % Favored : 64.22 % 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: 0.58 (0.39), residues: 512 helix: 1.70 (0.29), residues: 351 sheet: None (None), residues: 0 loop : -2.75 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 170 HIS 0.003 0.001 HIS A 370 PHE 0.008 0.001 PHE A 408 TYR 0.025 0.001 TYR A 497 ARG 0.002 0.000 ARG A 580 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 235) hydrogen bonds : angle 3.53490 ( 690) SS BOND : bond 0.00061 ( 1) SS BOND : angle 1.06501 ( 2) covalent geometry : bond 0.00245 ( 4283) covalent geometry : angle 0.56028 ( 5841) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.545 Fit side-chains REVERT: A 358 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.6874 (t80) REVERT: A 546 TYR cc_start: 0.6958 (OUTLIER) cc_final: 0.5856 (t80) outliers start: 19 outliers final: 16 residues processed: 82 average time/residue: 0.1722 time to fit residues: 18.8021 Evaluate side-chains 83 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 566 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.176592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.160734 restraints weight = 5653.679| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.21 r_work: 0.3672 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4284 Z= 0.118 Angle : 0.564 12.788 5843 Z= 0.273 Chirality : 0.040 0.188 642 Planarity : 0.004 0.067 715 Dihedral : 5.554 55.578 585 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.05 % Favored : 93.75 % Rotamer: Outliers : 5.50 % Allowed : 30.50 % Favored : 63.99 % 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: 0.62 (0.39), residues: 512 helix: 1.72 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -2.74 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 554 HIS 0.003 0.001 HIS A 370 PHE 0.009 0.001 PHE A 408 TYR 0.021 0.001 TYR A 497 ARG 0.003 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 235) hydrogen bonds : angle 3.53037 ( 690) SS BOND : bond 0.00166 ( 1) SS BOND : angle 1.06526 ( 2) covalent geometry : bond 0.00277 ( 4283) covalent geometry : angle 0.56366 ( 5841) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.490 Fit side-chains REVERT: A 231 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7055 (tt0) REVERT: A 358 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.6864 (t80) REVERT: A 546 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.5784 (t80) REVERT: A 590 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.6133 (tp) outliers start: 24 outliers final: 17 residues processed: 84 average time/residue: 0.1756 time to fit residues: 19.9126 Evaluate side-chains 86 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 590 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 44 optimal weight: 0.0870 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.176864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.160776 restraints weight = 5637.619| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.25 r_work: 0.3682 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4284 Z= 0.107 Angle : 0.567 12.820 5843 Z= 0.270 Chirality : 0.041 0.252 642 Planarity : 0.004 0.068 715 Dihedral : 5.478 55.749 585 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.27 % Favored : 94.53 % Rotamer: Outliers : 5.28 % Allowed : 30.50 % Favored : 64.22 % 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: 0.75 (0.39), residues: 512 helix: 1.83 (0.29), residues: 351 sheet: None (None), residues: 0 loop : -2.69 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 554 HIS 0.003 0.001 HIS A 370 PHE 0.008 0.001 PHE A 408 TYR 0.021 0.001 TYR A 497 ARG 0.003 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 235) hydrogen bonds : angle 3.48720 ( 690) SS BOND : bond 0.00161 ( 1) SS BOND : angle 0.95583 ( 2) covalent geometry : bond 0.00249 ( 4283) covalent geometry : angle 0.56648 ( 5841) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.874 Fit side-chains REVERT: A 231 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7083 (tt0) REVERT: A 273 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8160 (mm) REVERT: A 358 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.6875 (t80) REVERT: A 546 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.5715 (t80) outliers start: 23 outliers final: 18 residues processed: 84 average time/residue: 0.1843 time to fit residues: 20.8251 Evaluate side-chains 87 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 566 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 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 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.177404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.162281 restraints weight = 5556.837| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.11 r_work: 0.3684 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4284 Z= 0.113 Angle : 0.571 13.043 5843 Z= 0.272 Chirality : 0.040 0.225 642 Planarity : 0.004 0.067 715 Dihedral : 5.450 55.653 585 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.05 % Favored : 93.75 % Rotamer: Outliers : 5.96 % Allowed : 30.05 % Favored : 63.99 % 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: 0.79 (0.39), residues: 512 helix: 1.84 (0.29), residues: 351 sheet: None (None), residues: 0 loop : -2.65 (0.45), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 554 HIS 0.003 0.001 HIS A 370 PHE 0.009 0.001 PHE A 408 TYR 0.019 0.001 TYR A 497 ARG 0.006 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 235) hydrogen bonds : angle 3.47805 ( 690) SS BOND : bond 0.00191 ( 1) SS BOND : angle 0.94278 ( 2) covalent geometry : bond 0.00269 ( 4283) covalent geometry : angle 0.57076 ( 5841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2991.54 seconds wall clock time: 55 minutes 4.34 seconds (3304.34 seconds total)