Starting phenix.real_space_refine on Wed Sep 17 07:13:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j51_61139/09_2025/9j51_61139.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j51_61139/09_2025/9j51_61139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j51_61139/09_2025/9j51_61139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j51_61139/09_2025/9j51_61139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j51_61139/09_2025/9j51_61139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j51_61139/09_2025/9j51_61139.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.075 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 P 5 5.49 5 S 30 5.16 5 C 4454 2.51 5 N 1022 2.21 5 O 1070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6581 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3174 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 13, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3186 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 1 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'PC1': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.63, per 1000 atoms: 0.25 Number of scatterers: 6581 At special positions: 0 Unit cell: (126.26, 67.41, 74.9, 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 30 16.00 P 5 15.00 O 1070 8.00 N 1022 7.00 C 4454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 455.7 milliseconds Enol-peptide restraints added in 1.4 microseconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1448 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 231 through 258 removed outlier: 4.067A pdb=" N GLY A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE A 245 " --> pdb=" O CYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.237A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.619A pdb=" N PHE A 303 " --> pdb=" O HIS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 336 Processing helix chain 'A' and resid 337 through 340 Processing helix chain 'A' and resid 345 through 360 removed outlier: 4.486A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.600A pdb=" N THR A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.744A pdb=" N ASN A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 removed outlier: 4.278A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 471 Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 502 removed outlier: 4.021A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.563A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.505A pdb=" N THR A 545 " --> pdb=" O GLY A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 580 removed outlier: 3.541A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 618 removed outlier: 3.682A pdb=" N ALA A 593 " --> pdb=" O GLY A 589 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 3.904A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 removed outlier: 3.574A pdb=" N VAL B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 296 removed outlier: 3.874A pdb=" N ILE B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 337 Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 390 through 417 removed outlier: 3.656A pdb=" N ASN B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.652A pdb=" N ASP B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 502 removed outlier: 3.899A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.532A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 582 removed outlier: 3.953A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 582 " --> pdb=" O SER B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 617 removed outlier: 3.755A pdb=" N ALA B 593 " --> pdb=" O GLY B 589 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 3.703A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 612 " --> pdb=" O ASN B 608 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 613 " --> pdb=" O PHE B 609 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1263 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: 1.21 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1010 1.32 - 1.45: 2045 1.45 - 1.57: 3682 1.57 - 1.69: 8 1.69 - 1.82: 42 Bond restraints: 6787 Sorted by residual: bond pdb=" C THR A 582 " pdb=" O THR A 582 " ideal model delta sigma weight residual 1.236 1.252 -0.015 7.30e-03 1.88e+04 4.36e+00 bond pdb=" CA ILE B 454 " pdb=" CB ILE B 454 " ideal model delta sigma weight residual 1.539 1.529 0.010 5.40e-03 3.43e+04 3.73e+00 bond pdb=" CA ILE A 360 " pdb=" C ILE A 360 " ideal model delta sigma weight residual 1.524 1.515 0.009 8.60e-03 1.35e+04 1.18e+00 bond pdb=" C ALA A 597 " pdb=" N PRO A 598 " ideal model delta sigma weight residual 1.335 1.348 -0.014 1.28e-02 6.10e+03 1.14e+00 bond pdb=" N ARG B 624 " pdb=" CA ARG B 624 " ideal model delta sigma weight residual 1.458 1.478 -0.020 1.90e-02 2.77e+03 1.14e+00 ... (remaining 6782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 8914 1.37 - 2.74: 222 2.74 - 4.12: 36 4.12 - 5.49: 15 5.49 - 6.86: 2 Bond angle restraints: 9189 Sorted by residual: angle pdb=" C CYS A 453 " pdb=" N ILE A 454 " pdb=" CA ILE A 454 " ideal model delta sigma weight residual 120.33 123.55 -3.22 8.00e-01 1.56e+00 1.62e+01 angle pdb=" C PHE B 623 " pdb=" N ARG B 624 " pdb=" CA ARG B 624 " ideal model delta sigma weight residual 121.70 128.56 -6.86 1.80e+00 3.09e-01 1.45e+01 angle pdb=" CA LEU B 617 " pdb=" C LEU B 617 " pdb=" N ASN B 618 " ideal model delta sigma weight residual 117.79 113.59 4.20 1.22e+00 6.72e-01 1.19e+01 angle pdb=" N GLY B 621 " pdb=" CA GLY B 621 " pdb=" C GLY B 621 " ideal model delta sigma weight residual 114.64 110.11 4.53 1.40e+00 5.10e-01 1.05e+01 angle pdb=" N VAL B 346 " pdb=" CA VAL B 346 " pdb=" C VAL B 346 " ideal model delta sigma weight residual 113.39 109.12 4.27 1.47e+00 4.63e-01 8.44e+00 ... (remaining 9184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 3506 17.36 - 34.72: 296 34.72 - 52.08: 81 52.08 - 69.44: 24 69.44 - 86.81: 2 Dihedral angle restraints: 3909 sinusoidal: 1665 harmonic: 2244 Sorted by residual: dihedral pdb=" CA ALA A 384 " pdb=" C ALA A 384 " pdb=" N PRO A 385 " pdb=" CA PRO A 385 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA GLY A 242 " pdb=" C GLY A 242 " pdb=" N ILE A 243 " pdb=" CA ILE A 243 " ideal model delta harmonic sigma weight residual 180.00 159.91 20.09 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ASP B 538 " pdb=" CB ASP B 538 " pdb=" CG ASP B 538 " pdb=" OD1 ASP B 538 " ideal model delta sinusoidal sigma weight residual -30.00 -86.01 56.01 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 3906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 533 0.025 - 0.050: 279 0.050 - 0.075: 117 0.075 - 0.100: 39 0.100 - 0.125: 16 Chirality restraints: 984 Sorted by residual: chirality pdb=" CB VAL B 567 " pdb=" CA VAL B 567 " pdb=" CG1 VAL B 567 " pdb=" CG2 VAL B 567 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE A 342 " pdb=" N ILE A 342 " pdb=" C ILE A 342 " pdb=" CB ILE A 342 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA TRP B 266 " pdb=" N TRP B 266 " pdb=" C TRP B 266 " pdb=" CB TRP B 266 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 981 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 242 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C GLY A 242 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY A 242 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE A 243 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 384 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO A 385 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 385 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 385 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 460 " 0.010 2.00e-02 2.50e+03 9.01e-03 1.42e+00 pdb=" CG PHE A 460 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 460 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 460 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 460 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 460 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 460 " 0.003 2.00e-02 2.50e+03 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 92 2.65 - 3.22: 6358 3.22 - 3.78: 10583 3.78 - 4.34: 14411 4.34 - 4.90: 23475 Nonbonded interactions: 54919 Sorted by model distance: nonbonded pdb=" O LYS A 482 " pdb=" OG1 THR A 485 " model vdw 2.092 3.040 nonbonded pdb=" O ILE B 271 " pdb=" OH TYR B 352 " model vdw 2.127 3.040 nonbonded pdb=" O LYS B 482 " pdb=" OG1 THR B 485 " model vdw 2.169 3.040 nonbonded pdb=" O GLN A 576 " pdb=" OG1 THR A 580 " model vdw 2.234 3.040 nonbonded pdb=" OG SER A 370 " pdb=" O14 PC1 A 801 " model vdw 2.240 3.040 ... (remaining 54914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 231 through 802) selection = (chain 'B' and resid 231 through 802) } 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: 1.870 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.510 Find NCS groups from input model: 0.140 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:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 : 0.003 0.028 6788 Z= 0.154 Angle : 0.547 6.861 9189 Z= 0.314 Chirality : 0.038 0.125 984 Planarity : 0.004 0.051 1095 Dihedral : 14.554 86.805 2461 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.66 % Allowed : 8.12 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.31), residues: 754 helix: 1.43 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -3.02 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 570 TYR 0.012 0.001 TYR B 518 PHE 0.021 0.001 PHE A 460 TRP 0.012 0.001 TRP A 607 HIS 0.004 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6787) covalent geometry : angle 0.54669 ( 9189) hydrogen bonds : bond 0.12625 ( 424) hydrogen bonds : angle 5.33542 ( 1263) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8204 (mmm) cc_final: 0.7798 (mmm) REVERT: A 488 PHE cc_start: 0.8141 (m-80) cc_final: 0.7769 (m-80) REVERT: A 504 HIS cc_start: 0.7560 (t-90) cc_final: 0.7239 (t-170) REVERT: A 508 MET cc_start: 0.7767 (mmm) cc_final: 0.7428 (mmm) REVERT: A 511 PHE cc_start: 0.8307 (t80) cc_final: 0.8091 (t80) REVERT: A 528 TRP cc_start: 0.8360 (t-100) cc_final: 0.8116 (t-100) REVERT: B 280 GLU cc_start: 0.8722 (tt0) cc_final: 0.8327 (tt0) REVERT: B 283 PHE cc_start: 0.6853 (t80) cc_final: 0.6561 (t80) REVERT: B 413 MET cc_start: 0.5761 (mtp) cc_final: 0.5446 (mtm) REVERT: B 517 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: B 556 LYS cc_start: 0.7767 (mppt) cc_final: 0.7115 (mtpt) REVERT: B 615 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6903 (tm-30) REVERT: B 624 ARG cc_start: 0.6005 (OUTLIER) cc_final: 0.5096 (mmp80) outliers start: 18 outliers final: 8 residues processed: 172 average time/residue: 0.0884 time to fit residues: 19.9109 Evaluate side-chains 134 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 624 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.0170 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0070 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 540 ASN A 616 HIS B 294 GLN B 387 HIS B 399 GLN B 608 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.187045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.158841 restraints weight = 8939.323| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.16 r_work: 0.3689 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6788 Z= 0.136 Angle : 0.547 8.640 9189 Z= 0.294 Chirality : 0.040 0.142 984 Planarity : 0.004 0.048 1095 Dihedral : 11.506 60.183 1050 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.95 % Allowed : 12.11 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.31), residues: 754 helix: 1.40 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -2.97 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 236 TYR 0.016 0.002 TYR B 290 PHE 0.022 0.001 PHE B 394 TRP 0.012 0.001 TRP A 607 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6787) covalent geometry : angle 0.54694 ( 9189) hydrogen bonds : bond 0.04451 ( 424) hydrogen bonds : angle 4.47162 ( 1263) Misc. bond : bond 0.00098 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8206 (mmm) cc_final: 0.7485 (mmm) REVERT: A 488 PHE cc_start: 0.8198 (m-80) cc_final: 0.7745 (m-80) REVERT: A 504 HIS cc_start: 0.7574 (t-90) cc_final: 0.7177 (t-170) REVERT: A 511 PHE cc_start: 0.8282 (t80) cc_final: 0.8036 (t80) REVERT: A 528 TRP cc_start: 0.8388 (t-100) cc_final: 0.8079 (t-100) REVERT: B 283 PHE cc_start: 0.6760 (t80) cc_final: 0.6493 (t80) REVERT: B 409 ASP cc_start: 0.7466 (m-30) cc_final: 0.7139 (m-30) REVERT: B 413 MET cc_start: 0.5547 (mtp) cc_final: 0.5180 (mtp) REVERT: B 517 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7587 (m-10) REVERT: B 556 LYS cc_start: 0.7710 (mppt) cc_final: 0.7041 (mtpt) REVERT: B 615 GLU cc_start: 0.7460 (tm-30) cc_final: 0.6883 (tm-30) outliers start: 20 outliers final: 12 residues processed: 152 average time/residue: 0.0738 time to fit residues: 15.1122 Evaluate side-chains 138 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.0570 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 64 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.0980 overall best weight: 0.2498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.189462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.161468 restraints weight = 8853.000| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.17 r_work: 0.3732 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6788 Z= 0.114 Angle : 0.526 7.487 9189 Z= 0.278 Chirality : 0.039 0.130 984 Planarity : 0.004 0.046 1095 Dihedral : 11.016 59.094 1042 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.81 % Allowed : 12.41 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.31), residues: 754 helix: 1.57 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.90 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 236 TYR 0.016 0.001 TYR A 412 PHE 0.024 0.001 PHE B 394 TRP 0.011 0.001 TRP A 514 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 6787) covalent geometry : angle 0.52594 ( 9189) hydrogen bonds : bond 0.04064 ( 424) hydrogen bonds : angle 4.26948 ( 1263) Misc. bond : bond 0.00102 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 PHE cc_start: 0.8227 (m-80) cc_final: 0.7782 (m-80) REVERT: A 504 HIS cc_start: 0.7567 (t-90) cc_final: 0.7297 (t-170) REVERT: A 511 PHE cc_start: 0.8353 (t80) cc_final: 0.8058 (t80) REVERT: A 528 TRP cc_start: 0.8394 (t-100) cc_final: 0.8042 (t-100) REVERT: A 600 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6735 (mt-10) REVERT: B 283 PHE cc_start: 0.6549 (t80) cc_final: 0.6259 (t80) REVERT: B 409 ASP cc_start: 0.7654 (m-30) cc_final: 0.7257 (m-30) REVERT: B 517 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7630 (m-10) REVERT: B 556 LYS cc_start: 0.7647 (mppt) cc_final: 0.6989 (mtpt) REVERT: B 615 GLU cc_start: 0.7545 (tm-30) cc_final: 0.6896 (tm-30) outliers start: 19 outliers final: 12 residues processed: 155 average time/residue: 0.0744 time to fit residues: 15.9631 Evaluate side-chains 144 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** B 399 GLN ** 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 = 0.4135 r_free = 0.4135 target = 0.186345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.158058 restraints weight = 8939.130| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.17 r_work: 0.3678 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6788 Z= 0.142 Angle : 0.545 6.713 9189 Z= 0.286 Chirality : 0.040 0.174 984 Planarity : 0.004 0.043 1095 Dihedral : 11.251 60.068 1042 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.95 % Allowed : 13.88 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.31), residues: 754 helix: 1.44 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.83 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 236 TYR 0.018 0.002 TYR B 290 PHE 0.023 0.001 PHE B 394 TRP 0.014 0.001 TRP A 514 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6787) covalent geometry : angle 0.54513 ( 9189) hydrogen bonds : bond 0.04233 ( 424) hydrogen bonds : angle 4.29808 ( 1263) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 TYR cc_start: 0.8182 (m-80) cc_final: 0.7968 (m-80) REVERT: A 452 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7690 (tp40) REVERT: A 488 PHE cc_start: 0.8202 (m-80) cc_final: 0.7791 (m-80) REVERT: A 496 TYR cc_start: 0.8422 (t80) cc_final: 0.8119 (t80) REVERT: A 504 HIS cc_start: 0.7567 (t-90) cc_final: 0.7280 (t-170) REVERT: A 511 PHE cc_start: 0.8415 (t80) cc_final: 0.8207 (t80) REVERT: A 528 TRP cc_start: 0.8375 (t-100) cc_final: 0.8047 (t-100) REVERT: A 600 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6642 (mt-10) REVERT: B 283 PHE cc_start: 0.6788 (t80) cc_final: 0.6515 (t80) REVERT: B 409 ASP cc_start: 0.7435 (m-30) cc_final: 0.7226 (m-30) REVERT: B 517 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7671 (m-10) REVERT: B 615 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7028 (tm-30) outliers start: 20 outliers final: 16 residues processed: 155 average time/residue: 0.0832 time to fit residues: 17.4677 Evaluate side-chains 144 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 51 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.186827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.158499 restraints weight = 9065.835| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.18 r_work: 0.3690 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6788 Z= 0.134 Angle : 0.539 7.179 9189 Z= 0.282 Chirality : 0.040 0.199 984 Planarity : 0.004 0.049 1095 Dihedral : 11.249 60.529 1040 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.25 % Allowed : 14.33 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.31), residues: 754 helix: 1.46 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.77 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 472 TYR 0.019 0.002 TYR B 290 PHE 0.026 0.001 PHE B 394 TRP 0.014 0.001 TRP A 514 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6787) covalent geometry : angle 0.53910 ( 9189) hydrogen bonds : bond 0.04179 ( 424) hydrogen bonds : angle 4.29998 ( 1263) Misc. bond : bond 0.00078 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 488 PHE cc_start: 0.8175 (m-80) cc_final: 0.7766 (m-80) REVERT: A 496 TYR cc_start: 0.8382 (t80) cc_final: 0.8161 (t80) REVERT: A 504 HIS cc_start: 0.7751 (t-90) cc_final: 0.7448 (t70) REVERT: A 511 PHE cc_start: 0.8449 (t80) cc_final: 0.8191 (t80) REVERT: A 512 TYR cc_start: 0.8240 (m-10) cc_final: 0.7660 (m-10) REVERT: A 528 TRP cc_start: 0.8406 (t-100) cc_final: 0.7986 (t-100) REVERT: B 283 PHE cc_start: 0.6751 (t80) cc_final: 0.6416 (t80) REVERT: B 472 ARG cc_start: 0.7142 (mmm-85) cc_final: 0.6900 (mmm-85) REVERT: B 517 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7656 (m-10) REVERT: B 615 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6933 (tm-30) outliers start: 22 outliers final: 18 residues processed: 150 average time/residue: 0.0731 time to fit residues: 15.1756 Evaluate side-chains 142 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 2 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 GLN ** 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 = 0.4112 r_free = 0.4112 target = 0.184214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.155556 restraints weight = 8995.832| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.17 r_work: 0.3652 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6788 Z= 0.167 Angle : 0.566 7.357 9189 Z= 0.296 Chirality : 0.041 0.194 984 Planarity : 0.004 0.047 1095 Dihedral : 11.575 62.784 1040 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.55 % Allowed : 15.21 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.31), residues: 754 helix: 1.31 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -2.73 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 472 TYR 0.024 0.002 TYR B 290 PHE 0.027 0.001 PHE B 394 TRP 0.019 0.001 TRP A 514 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6787) covalent geometry : angle 0.56555 ( 9189) hydrogen bonds : bond 0.04447 ( 424) hydrogen bonds : angle 4.38251 ( 1263) Misc. bond : bond 0.00071 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 488 PHE cc_start: 0.8213 (m-80) cc_final: 0.7815 (m-80) REVERT: A 512 TYR cc_start: 0.8314 (m-10) cc_final: 0.7698 (m-10) REVERT: A 528 TRP cc_start: 0.8379 (t-100) cc_final: 0.7942 (t-100) REVERT: B 283 PHE cc_start: 0.6888 (t80) cc_final: 0.6255 (t80) REVERT: B 517 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7593 (m-80) REVERT: B 520 ILE cc_start: 0.6700 (tp) cc_final: 0.6473 (tp) REVERT: B 615 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7052 (tm-30) outliers start: 24 outliers final: 18 residues processed: 146 average time/residue: 0.0810 time to fit residues: 16.1736 Evaluate side-chains 145 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.185045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.157609 restraints weight = 8956.934| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.08 r_work: 0.3685 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6788 Z= 0.145 Angle : 0.555 7.782 9189 Z= 0.294 Chirality : 0.041 0.197 984 Planarity : 0.004 0.051 1095 Dihedral : 11.550 63.122 1040 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.25 % Allowed : 15.36 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.31), residues: 754 helix: 1.37 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -2.69 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 472 TYR 0.020 0.002 TYR A 496 PHE 0.028 0.001 PHE B 394 TRP 0.022 0.001 TRP A 514 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6787) covalent geometry : angle 0.55529 ( 9189) hydrogen bonds : bond 0.04371 ( 424) hydrogen bonds : angle 4.40926 ( 1263) Misc. bond : bond 0.00086 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.8069 (mmm-85) REVERT: A 488 PHE cc_start: 0.8195 (m-80) cc_final: 0.7783 (m-80) REVERT: A 504 HIS cc_start: 0.7917 (t-90) cc_final: 0.7547 (t-170) REVERT: A 528 TRP cc_start: 0.8357 (t-100) cc_final: 0.7939 (t-100) REVERT: B 283 PHE cc_start: 0.6834 (t80) cc_final: 0.6449 (t80) REVERT: B 517 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7563 (m-80) REVERT: B 615 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7014 (tm-30) outliers start: 22 outliers final: 19 residues processed: 147 average time/residue: 0.0795 time to fit residues: 15.9306 Evaluate side-chains 144 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.184803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.157218 restraints weight = 9046.536| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.09 r_work: 0.3684 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6788 Z= 0.146 Angle : 0.565 7.589 9189 Z= 0.298 Chirality : 0.041 0.212 984 Planarity : 0.004 0.047 1095 Dihedral : 11.598 63.564 1039 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.10 % Allowed : 16.40 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.31), residues: 754 helix: 1.35 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -2.64 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 472 TYR 0.027 0.002 TYR B 290 PHE 0.028 0.001 PHE B 394 TRP 0.017 0.001 TRP A 514 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6787) covalent geometry : angle 0.56453 ( 9189) hydrogen bonds : bond 0.04351 ( 424) hydrogen bonds : angle 4.40519 ( 1263) Misc. bond : bond 0.00083 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 488 PHE cc_start: 0.8188 (m-80) cc_final: 0.7780 (m-80) REVERT: A 528 TRP cc_start: 0.8313 (t-100) cc_final: 0.7895 (t-100) REVERT: B 283 PHE cc_start: 0.6885 (t80) cc_final: 0.6503 (t80) REVERT: B 517 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: B 615 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7039 (tm-30) outliers start: 21 outliers final: 18 residues processed: 150 average time/residue: 0.0739 time to fit residues: 15.1768 Evaluate side-chains 143 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 0.7980 chunk 49 optimal weight: 0.0370 chunk 58 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.184654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.156957 restraints weight = 9035.811| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.09 r_work: 0.3680 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6788 Z= 0.147 Angle : 0.575 7.819 9189 Z= 0.302 Chirality : 0.041 0.210 984 Planarity : 0.004 0.050 1095 Dihedral : 11.623 64.068 1039 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.69 % Allowed : 17.28 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.31), residues: 754 helix: 1.34 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -2.66 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 472 TYR 0.024 0.002 TYR B 290 PHE 0.028 0.001 PHE B 394 TRP 0.028 0.001 TRP A 514 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6787) covalent geometry : angle 0.57544 ( 9189) hydrogen bonds : bond 0.04371 ( 424) hydrogen bonds : angle 4.44342 ( 1263) Misc. bond : bond 0.00085 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 488 PHE cc_start: 0.8207 (m-80) cc_final: 0.7797 (m-80) REVERT: A 528 TRP cc_start: 0.8297 (t-100) cc_final: 0.7883 (t-100) REVERT: B 283 PHE cc_start: 0.6865 (t80) cc_final: 0.6506 (t80) REVERT: B 508 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6373 (ppp) REVERT: B 517 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: B 615 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7050 (tm-30) outliers start: 25 outliers final: 20 residues processed: 149 average time/residue: 0.0791 time to fit residues: 16.1442 Evaluate side-chains 148 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 545 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 73 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.185783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.158225 restraints weight = 8971.627| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.08 r_work: 0.3693 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6788 Z= 0.138 Angle : 0.580 7.977 9189 Z= 0.304 Chirality : 0.041 0.250 984 Planarity : 0.004 0.047 1095 Dihedral : 11.544 63.919 1039 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.40 % Allowed : 17.58 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.31), residues: 754 helix: 1.40 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.70 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 472 TYR 0.025 0.002 TYR A 496 PHE 0.029 0.001 PHE B 394 TRP 0.024 0.001 TRP A 514 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6787) covalent geometry : angle 0.58014 ( 9189) hydrogen bonds : bond 0.04285 ( 424) hydrogen bonds : angle 4.41909 ( 1263) Misc. bond : bond 0.00092 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 488 PHE cc_start: 0.8185 (m-80) cc_final: 0.7783 (m-80) REVERT: A 528 TRP cc_start: 0.8308 (t-100) cc_final: 0.7920 (t-100) REVERT: B 283 PHE cc_start: 0.6878 (t80) cc_final: 0.6505 (t80) REVERT: B 472 ARG cc_start: 0.7209 (mmm-85) cc_final: 0.6046 (tpp-160) REVERT: B 508 MET cc_start: 0.6569 (OUTLIER) cc_final: 0.6321 (ppp) REVERT: B 517 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7537 (m-80) REVERT: B 615 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7042 (tm-30) outliers start: 23 outliers final: 20 residues processed: 141 average time/residue: 0.0742 time to fit residues: 14.5353 Evaluate side-chains 143 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 68 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.184841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.157209 restraints weight = 8927.945| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.07 r_work: 0.3678 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6788 Z= 0.152 Angle : 0.594 7.848 9189 Z= 0.311 Chirality : 0.042 0.245 984 Planarity : 0.004 0.050 1095 Dihedral : 11.616 64.506 1039 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.55 % Allowed : 17.87 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.31), residues: 754 helix: 1.33 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.69 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 472 TYR 0.027 0.002 TYR A 496 PHE 0.029 0.001 PHE B 394 TRP 0.028 0.001 TRP A 514 HIS 0.002 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6787) covalent geometry : angle 0.59428 ( 9189) hydrogen bonds : bond 0.04386 ( 424) hydrogen bonds : angle 4.45717 ( 1263) Misc. bond : bond 0.00084 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1600.17 seconds wall clock time: 28 minutes 9.63 seconds (1689.63 seconds total)