Starting phenix.real_space_refine on Wed Sep 17 07:22:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j53_61141/09_2025/9j53_61141.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j53_61141/09_2025/9j53_61141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j53_61141/09_2025/9j53_61141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j53_61141/09_2025/9j53_61141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j53_61141/09_2025/9j53_61141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j53_61141/09_2025/9j53_61141.map" } resolution = 3.3 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= 0.061 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 6 5.49 5 S 30 5.16 5 C 4462 2.51 5 N 1024 2.21 5 O 1076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 6598 Number of models: 1 Model: "" Number of chains: 4 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: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3186 Classifications: {'peptide': 382} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 367} Chain breaks: 1 Chain: "B" 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: "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} Time building chain proxies: 1.79, per 1000 atoms: 0.27 Number of scatterers: 6598 At special positions: 0 Unit cell: (125.19, 69.55, 78.11, 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 6 15.00 O 1076 8.00 N 1024 7.00 C 4462 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: 0.63 Conformation dependent library (CDL) restraints added in 347.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 75.5% 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 'B' and resid 230 through 257 Processing helix chain 'B' and resid 265 through 295 removed outlier: 4.645A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.690A pdb=" N PHE B 303 " --> pdb=" O HIS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 336 Processing helix chain 'B' and resid 337 through 340 Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.537A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.636A pdb=" N THR B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 419 removed outlier: 3.606A pdb=" N ASN B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 469 Proline residue: B 455 - end of helix removed outlier: 3.740A pdb=" N ARG B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 500 removed outlier: 3.668A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.627A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 580 removed outlier: 3.675A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 562 " --> pdb=" O TYR B 558 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 578 " --> pdb=" O THR B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 615 Proline residue: B 598 - end of helix removed outlier: 3.656A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 256 removed outlier: 3.832A pdb=" N VAL A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 295 removed outlier: 5.166A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 304 removed outlier: 4.135A pdb=" N GLU A 304 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 337 Processing helix chain 'A' and resid 345 through 361 removed outlier: 4.264A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 359 " --> pdb=" O MET A 355 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A 361 " --> pdb=" O PHE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.786A pdb=" N PHE A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.814A pdb=" N ASN A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 417 removed outlier: 3.540A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.698A pdb=" N CYS A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 removed outlier: 3.685A pdb=" N ARG A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 503 removed outlier: 4.146A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.945A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 582 removed outlier: 4.394A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 618 Proline residue: A 598 - end of helix removed outlier: 3.664A pdb=" N LEU A 612 " --> pdb=" O ASN A 608 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.81 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: 986 1.32 - 1.44: 2069 1.44 - 1.57: 3695 1.57 - 1.69: 12 1.69 - 1.81: 42 Bond restraints: 6804 Sorted by residual: bond pdb=" C ALA B 337 " pdb=" N PRO B 338 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.47e-01 bond pdb=" CB GLN B 399 " pdb=" CG GLN B 399 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.45e-01 bond pdb=" C TYR B 347 " pdb=" N PRO B 348 " ideal model delta sigma weight residual 1.335 1.347 -0.011 1.36e-02 5.41e+03 6.86e-01 bond pdb=" CA ILE B 279 " pdb=" C ILE B 279 " ideal model delta sigma weight residual 1.524 1.514 0.010 1.22e-02 6.72e+03 6.66e-01 bond pdb=" CB PRO A 385 " pdb=" CG PRO A 385 " ideal model delta sigma weight residual 1.492 1.453 0.039 5.00e-02 4.00e+02 6.10e-01 ... (remaining 6799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 8965 1.52 - 3.04: 209 3.04 - 4.56: 27 4.56 - 6.08: 10 6.08 - 7.60: 3 Bond angle restraints: 9214 Sorted by residual: angle pdb=" N ILE B 577 " pdb=" CA ILE B 577 " pdb=" C ILE B 577 " ideal model delta sigma weight residual 113.00 109.53 3.47 1.30e+00 5.92e-01 7.10e+00 angle pdb=" C SER B 402 " pdb=" N LEU B 403 " pdb=" CA LEU B 403 " ideal model delta sigma weight residual 122.73 118.80 3.93 1.61e+00 3.86e-01 5.96e+00 angle pdb=" C GLY B 621 " pdb=" N GLU B 622 " pdb=" CA GLU B 622 " ideal model delta sigma weight residual 122.40 125.93 -3.53 1.45e+00 4.76e-01 5.91e+00 angle pdb=" N GLY A 296 " pdb=" CA GLY A 296 " pdb=" C GLY A 296 " ideal model delta sigma weight residual 113.18 118.53 -5.35 2.37e+00 1.78e-01 5.09e+00 angle pdb=" CA LEU B 259 " pdb=" CB LEU B 259 " pdb=" CG LEU B 259 " ideal model delta sigma weight residual 116.30 123.90 -7.60 3.50e+00 8.16e-02 4.72e+00 ... (remaining 9209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3529 18.00 - 35.99: 278 35.99 - 53.99: 90 53.99 - 71.98: 15 71.98 - 89.98: 6 Dihedral angle restraints: 3918 sinusoidal: 1668 harmonic: 2250 Sorted by residual: dihedral pdb=" CA ASN B 298 " pdb=" C ASN B 298 " pdb=" N HIS B 299 " pdb=" CA HIS B 299 " ideal model delta harmonic sigma weight residual -180.00 -157.60 -22.40 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ILE A 302 " pdb=" C ILE A 302 " pdb=" N PHE A 303 " pdb=" CA PHE A 303 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA PHE A 303 " pdb=" C PHE A 303 " pdb=" N GLU A 304 " pdb=" CA GLU A 304 " ideal model delta harmonic sigma weight residual -180.00 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 3915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 579 0.029 - 0.057: 267 0.057 - 0.086: 102 0.086 - 0.114: 35 0.114 - 0.143: 3 Chirality restraints: 986 Sorted by residual: chirality pdb=" CA TRP A 266 " pdb=" N TRP A 266 " pdb=" C TRP A 266 " pdb=" CB TRP A 266 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.08e-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 3.49e-01 chirality pdb=" CA PRO B 554 " pdb=" N PRO B 554 " pdb=" C PRO B 554 " pdb=" CB PRO B 554 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 983 not shown) Planarity restraints: 1098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 337 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO B 338 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 561 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C CYS A 561 " 0.031 2.00e-02 2.50e+03 pdb=" O CYS A 561 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 562 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 563 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C ILE A 563 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE A 563 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 564 " 0.010 2.00e-02 2.50e+03 ... (remaining 1095 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 119 2.67 - 3.23: 6919 3.23 - 3.79: 10613 3.79 - 4.34: 14363 4.34 - 4.90: 23141 Nonbonded interactions: 55155 Sorted by model distance: nonbonded pdb=" O LYS A 482 " pdb=" OG1 THR A 485 " model vdw 2.117 3.040 nonbonded pdb=" O LYS B 482 " pdb=" OG1 THR B 485 " model vdw 2.123 3.040 nonbonded pdb=" O ILE A 551 " pdb=" OH TYR A 559 " model vdw 2.131 3.040 nonbonded pdb=" O ARG B 466 " pdb=" OG1 THR B 470 " model vdw 2.163 3.040 nonbonded pdb=" O TRP A 395 " pdb=" NE2 GLN A 399 " model vdw 2.174 3.120 ... (remaining 55150 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.500 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.080 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 0.039 6805 Z= 0.156 Angle : 0.575 7.601 9214 Z= 0.321 Chirality : 0.038 0.143 986 Planarity : 0.004 0.049 1098 Dihedral : 14.752 89.975 2466 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.13 % Allowed : 9.00 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.49 (0.31), residues: 756 helix: 0.71 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -2.81 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 465 TYR 0.010 0.001 TYR B 518 PHE 0.014 0.001 PHE A 605 TRP 0.012 0.001 TRP B 266 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6804) covalent geometry : angle 0.57489 ( 9214) hydrogen bonds : bond 0.15151 ( 413) hydrogen bonds : angle 6.02296 ( 1233) Misc. bond : bond 0.00107 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.256 Fit side-chains REVERT: B 283 PHE cc_start: 0.7347 (t80) cc_final: 0.6946 (t80) REVERT: B 345 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6790 (m-80) REVERT: B 408 MET cc_start: 0.8108 (mmm) cc_final: 0.7793 (mmm) REVERT: B 415 CYS cc_start: 0.8719 (t) cc_final: 0.8372 (p) REVERT: B 452 GLN cc_start: 0.9122 (tp40) cc_final: 0.8224 (tp40) REVERT: B 462 GLN cc_start: 0.8359 (mt0) cc_final: 0.7975 (mt0) REVERT: B 599 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8120 (mm) REVERT: A 290 TYR cc_start: 0.8364 (t80) cc_final: 0.8114 (t80) REVERT: A 308 ARG cc_start: 0.7489 (ptt180) cc_final: 0.7238 (ptt-90) REVERT: A 379 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6315 (t80) REVERT: A 408 MET cc_start: 0.7630 (mmt) cc_final: 0.7382 (mmt) REVERT: A 409 ASP cc_start: 0.6501 (OUTLIER) cc_final: 0.5568 (t70) REVERT: A 410 LEU cc_start: 0.7347 (tt) cc_final: 0.7090 (tt) REVERT: A 461 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8465 (tp) REVERT: A 495 LEU cc_start: 0.9322 (mm) cc_final: 0.8887 (mm) REVERT: A 548 ARG cc_start: 0.7987 (ptp90) cc_final: 0.7469 (ptt90) REVERT: A 565 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: A 605 PHE cc_start: 0.7836 (t80) cc_final: 0.7440 (t80) outliers start: 28 outliers final: 10 residues processed: 224 average time/residue: 0.0768 time to fit residues: 23.4703 Evaluate side-chains 183 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 609 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.1980 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0670 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 overall best weight: 0.1716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 ASN B 608 ASN B 618 ASN A 288 ASN A 310 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN A 619 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.192008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.168514 restraints weight = 10801.083| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.74 r_work: 0.3991 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6805 Z= 0.137 Angle : 0.599 8.376 9214 Z= 0.313 Chirality : 0.041 0.199 986 Planarity : 0.005 0.048 1098 Dihedral : 12.639 76.367 1066 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.69 % Allowed : 14.45 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.10 (0.31), residues: 756 helix: 1.20 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -2.86 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 548 TYR 0.012 0.001 TYR A 417 PHE 0.016 0.001 PHE B 391 TRP 0.021 0.002 TRP B 528 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6804) covalent geometry : angle 0.59880 ( 9214) hydrogen bonds : bond 0.04881 ( 413) hydrogen bonds : angle 4.38106 ( 1233) Misc. bond : bond 0.00106 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 PHE cc_start: 0.7676 (t80) cc_final: 0.7432 (t80) REVERT: B 345 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.6273 (m-80) REVERT: B 415 CYS cc_start: 0.8563 (t) cc_final: 0.8272 (p) REVERT: B 452 GLN cc_start: 0.9017 (tp40) cc_final: 0.8777 (tp40) REVERT: A 290 TYR cc_start: 0.8273 (t80) cc_final: 0.8011 (t80) REVERT: A 308 ARG cc_start: 0.7384 (ptt180) cc_final: 0.7040 (ptt-90) REVERT: A 379 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.6211 (t80) REVERT: A 409 ASP cc_start: 0.5891 (OUTLIER) cc_final: 0.4841 (t70) REVERT: A 472 ARG cc_start: 0.4811 (tpt170) cc_final: 0.4459 (mmm160) REVERT: A 477 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7676 (mm) REVERT: A 495 LEU cc_start: 0.9241 (mm) cc_final: 0.8818 (mm) REVERT: A 603 ARG cc_start: 0.7989 (tmm-80) cc_final: 0.7648 (tmm-80) outliers start: 25 outliers final: 9 residues processed: 212 average time/residue: 0.0717 time to fit residues: 21.0880 Evaluate side-chains 205 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 609 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 53 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 0.0370 chunk 4 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.4369 r_free = 0.4369 target = 0.190980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.166555 restraints weight = 10573.812| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.81 r_work: 0.3971 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6805 Z= 0.137 Angle : 0.586 8.572 9214 Z= 0.304 Chirality : 0.041 0.188 986 Planarity : 0.004 0.045 1098 Dihedral : 12.113 77.400 1046 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.13 % Allowed : 17.11 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.20 (0.31), residues: 756 helix: 1.26 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.73 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 611 TYR 0.009 0.001 TYR B 518 PHE 0.021 0.001 PHE A 596 TRP 0.018 0.002 TRP B 528 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6804) covalent geometry : angle 0.58639 ( 9214) hydrogen bonds : bond 0.04681 ( 413) hydrogen bonds : angle 4.36931 ( 1233) Misc. bond : bond 0.00128 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 244 PHE cc_start: 0.7696 (t80) cc_final: 0.7421 (t80) REVERT: B 415 CYS cc_start: 0.8592 (t) cc_final: 0.8310 (p) REVERT: A 283 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.7104 (t80) REVERT: A 290 TYR cc_start: 0.8307 (t80) cc_final: 0.7960 (t80) REVERT: A 308 ARG cc_start: 0.7403 (ptt180) cc_final: 0.7134 (ptt-90) REVERT: A 379 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.6307 (t80) REVERT: A 409 ASP cc_start: 0.5634 (OUTLIER) cc_final: 0.4476 (t70) REVERT: A 477 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7662 (mm) REVERT: A 495 LEU cc_start: 0.9302 (mm) cc_final: 0.8854 (mm) REVERT: A 603 ARG cc_start: 0.8042 (tmm-80) cc_final: 0.7686 (tmm-80) outliers start: 28 outliers final: 15 residues processed: 197 average time/residue: 0.0797 time to fit residues: 21.5708 Evaluate side-chains 191 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 609 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 25 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 71 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.189942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.166310 restraints weight = 10863.890| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 2.73 r_work: 0.3965 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6805 Z= 0.143 Angle : 0.595 8.831 9214 Z= 0.308 Chirality : 0.041 0.159 986 Planarity : 0.004 0.045 1098 Dihedral : 12.102 79.556 1042 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.13 % Allowed : 18.44 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.20 (0.31), residues: 756 helix: 1.24 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.68 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 448 TYR 0.010 0.001 TYR B 518 PHE 0.027 0.001 PHE A 596 TRP 0.018 0.002 TRP B 528 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6804) covalent geometry : angle 0.59516 ( 9214) hydrogen bonds : bond 0.04602 ( 413) hydrogen bonds : angle 4.35056 ( 1233) Misc. bond : bond 0.00164 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 415 CYS cc_start: 0.8597 (t) cc_final: 0.8308 (p) REVERT: A 253 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5900 (mm) REVERT: A 283 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.7065 (t80) REVERT: A 290 TYR cc_start: 0.8334 (t80) cc_final: 0.7932 (t80) REVERT: A 308 ARG cc_start: 0.7398 (ptt180) cc_final: 0.7118 (ptt-90) REVERT: A 379 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.6291 (t80) REVERT: A 409 ASP cc_start: 0.5352 (OUTLIER) cc_final: 0.4143 (t0) REVERT: A 477 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7685 (mm) REVERT: A 489 MET cc_start: 0.6818 (tpt) cc_final: 0.6614 (tpt) REVERT: A 495 LEU cc_start: 0.9310 (mm) cc_final: 0.8865 (mm) REVERT: A 603 ARG cc_start: 0.8069 (tmm-80) cc_final: 0.7689 (tmm-80) REVERT: A 615 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7783 (tm-30) outliers start: 28 outliers final: 17 residues processed: 197 average time/residue: 0.0753 time to fit residues: 20.6489 Evaluate side-chains 192 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 609 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 30 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.190576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.166802 restraints weight = 10892.877| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.77 r_work: 0.3983 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6805 Z= 0.134 Angle : 0.588 9.269 9214 Z= 0.304 Chirality : 0.041 0.161 986 Planarity : 0.004 0.045 1098 Dihedral : 12.036 79.267 1042 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.13 % Allowed : 19.62 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.27 (0.31), residues: 756 helix: 1.28 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.63 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 448 TYR 0.009 0.001 TYR B 518 PHE 0.028 0.001 PHE A 596 TRP 0.017 0.002 TRP B 528 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6804) covalent geometry : angle 0.58813 ( 9214) hydrogen bonds : bond 0.04485 ( 413) hydrogen bonds : angle 4.31373 ( 1233) Misc. bond : bond 0.00157 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 244 PHE cc_start: 0.7667 (t80) cc_final: 0.7409 (t80) REVERT: B 415 CYS cc_start: 0.8570 (t) cc_final: 0.8299 (p) REVERT: A 253 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5880 (mm) REVERT: A 283 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.7112 (t80) REVERT: A 290 TYR cc_start: 0.8330 (t80) cc_final: 0.7923 (t80) REVERT: A 308 ARG cc_start: 0.7349 (ptt180) cc_final: 0.7069 (ptt-90) REVERT: A 379 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.6255 (t80) REVERT: A 409 ASP cc_start: 0.5359 (OUTLIER) cc_final: 0.4221 (t70) REVERT: A 477 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7691 (mm) REVERT: A 489 MET cc_start: 0.6914 (tpt) cc_final: 0.6662 (tpt) REVERT: A 495 LEU cc_start: 0.9303 (mm) cc_final: 0.8853 (mm) REVERT: A 603 ARG cc_start: 0.8025 (tmm-80) cc_final: 0.7635 (tmm-80) REVERT: A 615 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7734 (tm-30) outliers start: 28 outliers final: 18 residues processed: 206 average time/residue: 0.0678 time to fit residues: 19.5518 Evaluate side-chains 197 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 609 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 62 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.190550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.166209 restraints weight = 11106.922| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.82 r_work: 0.3973 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6805 Z= 0.154 Angle : 0.627 9.324 9214 Z= 0.322 Chirality : 0.045 0.328 986 Planarity : 0.004 0.045 1098 Dihedral : 12.201 79.413 1042 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.28 % Allowed : 20.21 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.22 (0.31), residues: 756 helix: 1.23 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.60 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 604 TYR 0.010 0.001 TYR B 518 PHE 0.032 0.001 PHE A 596 TRP 0.021 0.002 TRP B 528 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6804) covalent geometry : angle 0.62674 ( 9214) hydrogen bonds : bond 0.04589 ( 413) hydrogen bonds : angle 4.42946 ( 1233) Misc. bond : bond 0.00151 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: B 415 CYS cc_start: 0.8552 (t) cc_final: 0.8302 (p) REVERT: A 253 LEU cc_start: 0.6105 (OUTLIER) cc_final: 0.5827 (mm) REVERT: A 283 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7126 (t80) REVERT: A 290 TYR cc_start: 0.8270 (t80) cc_final: 0.7823 (t80) REVERT: A 308 ARG cc_start: 0.7406 (ptt180) cc_final: 0.7127 (ptt-90) REVERT: A 379 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6298 (t80) REVERT: A 409 ASP cc_start: 0.5337 (OUTLIER) cc_final: 0.4208 (t70) REVERT: A 477 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7731 (mm) REVERT: A 489 MET cc_start: 0.7088 (tpt) cc_final: 0.6826 (tpt) REVERT: A 495 LEU cc_start: 0.9314 (mm) cc_final: 0.8875 (mm) REVERT: A 615 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7718 (tm-30) outliers start: 29 outliers final: 18 residues processed: 194 average time/residue: 0.0596 time to fit residues: 16.2863 Evaluate side-chains 193 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 609 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.4363 r_free = 0.4363 target = 0.190360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.166972 restraints weight = 10797.880| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.72 r_work: 0.3982 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6805 Z= 0.144 Angle : 0.639 10.588 9214 Z= 0.328 Chirality : 0.043 0.232 986 Planarity : 0.004 0.045 1098 Dihedral : 12.101 78.520 1042 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 4.42 % Allowed : 21.09 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.30 (0.31), residues: 756 helix: 1.27 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.53 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 603 TYR 0.013 0.001 TYR A 367 PHE 0.028 0.001 PHE A 596 TRP 0.023 0.002 TRP B 528 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6804) covalent geometry : angle 0.63853 ( 9214) hydrogen bonds : bond 0.04620 ( 413) hydrogen bonds : angle 4.42801 ( 1233) Misc. bond : bond 0.00151 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: B 415 CYS cc_start: 0.8491 (t) cc_final: 0.8275 (p) REVERT: A 253 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5828 (mm) REVERT: A 283 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.7062 (t80) REVERT: A 290 TYR cc_start: 0.8239 (t80) cc_final: 0.7775 (t80) REVERT: A 308 ARG cc_start: 0.7340 (ptt180) cc_final: 0.7057 (ptt-90) REVERT: A 379 PHE cc_start: 0.6652 (OUTLIER) cc_final: 0.6310 (t80) REVERT: A 409 ASP cc_start: 0.5251 (OUTLIER) cc_final: 0.4148 (t70) REVERT: A 477 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7705 (mm) REVERT: A 489 MET cc_start: 0.7038 (tpt) cc_final: 0.6798 (tpt) REVERT: A 495 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8833 (mm) REVERT: A 615 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7689 (tm-30) outliers start: 30 outliers final: 19 residues processed: 194 average time/residue: 0.0687 time to fit residues: 18.6001 Evaluate side-chains 197 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 609 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 55 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 59 optimal weight: 0.0980 chunk 52 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.191064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.167588 restraints weight = 10952.345| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.75 r_work: 0.3988 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6805 Z= 0.136 Angle : 0.624 10.236 9214 Z= 0.321 Chirality : 0.042 0.202 986 Planarity : 0.004 0.046 1098 Dihedral : 11.988 77.728 1042 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.28 % Allowed : 22.42 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.29 (0.31), residues: 756 helix: 1.24 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -2.67 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 448 TYR 0.012 0.001 TYR A 367 PHE 0.022 0.001 PHE A 605 TRP 0.027 0.002 TRP B 528 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6804) covalent geometry : angle 0.62355 ( 9214) hydrogen bonds : bond 0.04526 ( 413) hydrogen bonds : angle 4.40599 ( 1233) Misc. bond : bond 0.00144 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 415 CYS cc_start: 0.8485 (t) cc_final: 0.8277 (p) REVERT: A 253 LEU cc_start: 0.6119 (OUTLIER) cc_final: 0.5817 (mm) REVERT: A 283 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7094 (t80) REVERT: A 308 ARG cc_start: 0.7350 (ptt180) cc_final: 0.7081 (ptt-90) REVERT: A 379 PHE cc_start: 0.6627 (OUTLIER) cc_final: 0.6334 (t80) REVERT: A 409 ASP cc_start: 0.5163 (OUTLIER) cc_final: 0.4038 (t70) REVERT: A 477 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7623 (mm) REVERT: A 489 MET cc_start: 0.7005 (tpt) cc_final: 0.6764 (tpt) REVERT: A 495 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8820 (mm) REVERT: A 615 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7628 (tm-30) outliers start: 29 outliers final: 18 residues processed: 190 average time/residue: 0.0629 time to fit residues: 16.9430 Evaluate side-chains 197 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 609 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.192337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.168376 restraints weight = 11012.385| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.81 r_work: 0.4001 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6805 Z= 0.138 Angle : 0.632 10.581 9214 Z= 0.327 Chirality : 0.043 0.183 986 Planarity : 0.004 0.045 1098 Dihedral : 12.006 78.162 1042 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.42 % Allowed : 22.86 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.30 (0.31), residues: 756 helix: 1.24 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -2.64 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 448 TYR 0.012 0.001 TYR A 367 PHE 0.026 0.001 PHE A 357 TRP 0.029 0.002 TRP B 528 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6804) covalent geometry : angle 0.63220 ( 9214) hydrogen bonds : bond 0.04476 ( 413) hydrogen bonds : angle 4.41843 ( 1233) Misc. bond : bond 0.00150 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 244 PHE cc_start: 0.7687 (t80) cc_final: 0.7395 (t80) REVERT: A 253 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5842 (mm) REVERT: A 308 ARG cc_start: 0.7322 (ptt180) cc_final: 0.7038 (ptt-90) REVERT: A 379 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.6351 (t80) REVERT: A 409 ASP cc_start: 0.5415 (OUTLIER) cc_final: 0.4244 (t70) REVERT: A 477 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7635 (mm) REVERT: A 495 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8881 (mm) REVERT: A 615 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7651 (tm-30) outliers start: 30 outliers final: 19 residues processed: 190 average time/residue: 0.0607 time to fit residues: 16.2930 Evaluate side-chains 194 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 609 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 64 optimal weight: 0.0000 chunk 59 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.4368 r_free = 0.4368 target = 0.191392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.167262 restraints weight = 10973.115| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.86 r_work: 0.3953 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6805 Z= 0.142 Angle : 0.657 10.758 9214 Z= 0.339 Chirality : 0.044 0.192 986 Planarity : 0.004 0.046 1098 Dihedral : 11.999 78.106 1042 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.54 % Allowed : 23.89 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.23 (0.31), residues: 756 helix: 1.18 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -2.64 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 448 TYR 0.021 0.001 TYR A 290 PHE 0.027 0.001 PHE B 386 TRP 0.027 0.002 TRP B 528 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6804) covalent geometry : angle 0.65657 ( 9214) hydrogen bonds : bond 0.04488 ( 413) hydrogen bonds : angle 4.42119 ( 1233) Misc. bond : bond 0.00146 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 253 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5821 (mm) REVERT: A 283 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7058 (t80) REVERT: A 290 TYR cc_start: 0.8011 (t80) cc_final: 0.7777 (t80) REVERT: A 308 ARG cc_start: 0.7473 (ptt180) cc_final: 0.7213 (ptt-90) REVERT: A 379 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.6366 (t80) REVERT: A 409 ASP cc_start: 0.5322 (OUTLIER) cc_final: 0.4404 (t70) REVERT: A 477 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7641 (mm) REVERT: A 495 LEU cc_start: 0.9270 (mm) cc_final: 0.8883 (mm) REVERT: A 615 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7664 (tm-30) outliers start: 24 outliers final: 17 residues processed: 181 average time/residue: 0.0648 time to fit residues: 16.9108 Evaluate side-chains 189 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 609 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.4350 r_free = 0.4350 target = 0.189630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.165335 restraints weight = 10904.265| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.83 r_work: 0.3931 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6805 Z= 0.163 Angle : 0.677 10.543 9214 Z= 0.350 Chirality : 0.044 0.185 986 Planarity : 0.004 0.045 1098 Dihedral : 12.145 79.772 1042 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.69 % Allowed : 24.04 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.07 (0.31), residues: 756 helix: 1.05 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -2.66 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 448 TYR 0.020 0.001 TYR A 290 PHE 0.026 0.002 PHE B 386 TRP 0.041 0.002 TRP A 514 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6804) covalent geometry : angle 0.67728 ( 9214) hydrogen bonds : bond 0.04645 ( 413) hydrogen bonds : angle 4.50776 ( 1233) Misc. bond : bond 0.00160 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1620.40 seconds wall clock time: 28 minutes 35.24 seconds (1715.24 seconds total)