Starting phenix.real_space_refine on Fri Dec 27 08:00:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jys_36730/12_2024/8jys_36730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jys_36730/12_2024/8jys_36730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jys_36730/12_2024/8jys_36730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jys_36730/12_2024/8jys_36730.map" model { file = "/net/cci-nas-00/data/ceres_data/8jys_36730/12_2024/8jys_36730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jys_36730/12_2024/8jys_36730.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2271 2.51 5 N 587 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3522 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 241 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain breaks: 1 Chain: "B" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1514 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 253 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain breaks: 1 Chain: "D" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1514 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.90, per 1000 atoms: 0.82 Number of scatterers: 3522 At special positions: 0 Unit cell: (90.094, 67.36, 119.564, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 648 8.00 N 587 7.00 C 2271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 440.9 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 822 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 5 sheets defined 11.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.391A pdb=" N LEU B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 4.104A pdb=" N ILE B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 411' Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 383 through 388 Processing helix chain 'D' and resid 404 through 410 removed outlier: 3.808A pdb=" N VAL D 407 " --> pdb=" O GLY D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.709A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.709A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA4, first strand: chain 'D' and resid 356 through 358 removed outlier: 4.195A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.969A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) 56 hydrogen bonds defined for protein. 129 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: 0.73 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1112 1.34 - 1.47: 1024 1.47 - 1.59: 1473 1.59 - 1.72: 0 1.72 - 1.84: 16 Bond restraints: 3625 Sorted by residual: bond pdb=" N LEU C 109 " pdb=" CA LEU C 109 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.49e-02 4.50e+03 5.38e+00 bond pdb=" C GLU A 57 " pdb=" N PRO A 58 " ideal model delta sigma weight residual 1.328 1.353 -0.025 1.26e-02 6.30e+03 3.84e+00 bond pdb=" C ALA D 520 " pdb=" N PRO D 521 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.33e-02 5.65e+03 3.07e+00 bond pdb=" C PRO B 373 " pdb=" O PRO B 373 " ideal model delta sigma weight residual 1.235 1.218 0.017 1.30e-02 5.92e+03 1.81e+00 bond pdb=" C PRO D 521 " pdb=" O PRO D 521 " ideal model delta sigma weight residual 1.233 1.218 0.015 1.23e-02 6.61e+03 1.46e+00 ... (remaining 3620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 4704 2.01 - 4.03: 179 4.03 - 6.04: 33 6.04 - 8.06: 11 8.06 - 10.07: 3 Bond angle restraints: 4930 Sorted by residual: angle pdb=" C ASN D 422 " pdb=" N TYR D 423 " pdb=" CA TYR D 423 " ideal model delta sigma weight residual 121.54 131.56 -10.02 1.91e+00 2.74e-01 2.75e+01 angle pdb=" CA TYR D 423 " pdb=" CB TYR D 423 " pdb=" CG TYR D 423 " ideal model delta sigma weight residual 113.90 120.74 -6.84 1.80e+00 3.09e-01 1.44e+01 angle pdb=" N SER B 366 " pdb=" CA SER B 366 " pdb=" C SER B 366 " ideal model delta sigma weight residual 113.43 108.71 4.72 1.26e+00 6.30e-01 1.40e+01 angle pdb=" CB LYS B 356 " pdb=" CG LYS B 356 " pdb=" CD LYS B 356 " ideal model delta sigma weight residual 111.30 119.15 -7.85 2.30e+00 1.89e-01 1.16e+01 angle pdb=" C GLU B 465 " pdb=" CA GLU B 465 " pdb=" CB GLU B 465 " ideal model delta sigma weight residual 113.37 108.12 5.25 1.61e+00 3.86e-01 1.06e+01 ... (remaining 4925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 1704 16.01 - 32.01: 307 32.01 - 48.02: 81 48.02 - 64.02: 20 64.02 - 80.02: 6 Dihedral angle restraints: 2118 sinusoidal: 826 harmonic: 1292 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -21.65 -64.35 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 46.59 46.41 1 1.00e+01 1.00e-02 2.98e+01 dihedral pdb=" CB CYS D 379 " pdb=" SG CYS D 379 " pdb=" SG CYS D 432 " pdb=" CB CYS D 432 " ideal model delta sinusoidal sigma weight residual 93.00 52.27 40.73 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 2115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 272 0.031 - 0.061: 132 0.061 - 0.092: 71 0.092 - 0.123: 30 0.123 - 0.153: 4 Chirality restraints: 509 Sorted by residual: chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA VAL D 511 " pdb=" N VAL D 511 " pdb=" C VAL D 511 " pdb=" CB VAL D 511 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA ILE B 402 " pdb=" N ILE B 402 " pdb=" C ILE B 402 " pdb=" CB ILE B 402 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 506 not shown) Planarity restraints: 644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 372 " 0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO D 373 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO D 373 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 373 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 57 " 0.043 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO C 58 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 58 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 58 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 509 " -0.184 9.50e-02 1.11e+02 8.27e-02 4.24e+00 pdb=" NE ARG D 509 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D 509 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 509 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 509 " -0.005 2.00e-02 2.50e+03 ... (remaining 641 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 349 2.74 - 3.28: 3830 3.28 - 3.82: 5469 3.82 - 4.36: 6023 4.36 - 4.90: 9633 Nonbonded interactions: 25304 Sorted by model distance: nonbonded pdb=" O PHE D 347 " pdb=" OH TYR D 451 " model vdw 2.197 3.040 nonbonded pdb=" OG SER D 383 " pdb=" NZ LYS D 386 " model vdw 2.201 3.120 nonbonded pdb=" OG SER D 438 " pdb=" OD1 ASP D 442 " model vdw 2.217 3.040 nonbonded pdb=" NZ LYS D 478 " pdb=" O PRO D 479 " model vdw 2.244 3.120 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.245 3.040 ... (remaining 25299 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' selection = (chain 'C' and resid 49 through 116) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.140 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: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 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 : 0.004 0.038 3625 Z= 0.257 Angle : 0.964 10.071 4930 Z= 0.516 Chirality : 0.048 0.153 509 Planarity : 0.008 0.083 644 Dihedral : 17.514 80.024 1272 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 1.18 % Allowed : 12.71 % Favored : 86.12 % Rotamer: Outliers : 1.88 % Allowed : 38.34 % Favored : 59.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.38), residues: 425 helix: -2.42 (0.72), residues: 44 sheet: -0.81 (0.64), residues: 68 loop : -2.90 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.029 0.002 PHE B 456 TYR 0.022 0.002 TYR B 508 ARG 0.012 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 374 PHE cc_start: 0.7908 (t80) cc_final: 0.7666 (m-80) REVERT: B 451 TYR cc_start: 0.7749 (m-80) cc_final: 0.7514 (m-80) REVERT: D 516 GLU cc_start: 0.7900 (tp30) cc_final: 0.7482 (tm-30) outliers start: 7 outliers final: 4 residues processed: 105 average time/residue: 0.2188 time to fit residues: 26.4991 Evaluate side-chains 102 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN D 422 ASN D 474 GLN D 481 ASN D 487 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3625 Z= 0.221 Angle : 0.762 12.048 4930 Z= 0.383 Chirality : 0.046 0.159 509 Planarity : 0.006 0.052 644 Dihedral : 5.630 20.140 492 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 1.18 % Allowed : 11.29 % Favored : 87.53 % Rotamer: Outliers : 0.54 % Allowed : 5.36 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.38), residues: 425 helix: -3.54 (0.49), residues: 46 sheet: -0.45 (0.63), residues: 64 loop : -2.49 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 436 HIS 0.007 0.002 HIS B 505 PHE 0.023 0.002 PHE D 375 TYR 0.023 0.002 TYR B 423 ARG 0.009 0.001 ARG D 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 ARG cc_start: 0.7526 (mtt180) cc_final: 0.7322 (mtt90) REVERT: D 335 LEU cc_start: 0.8971 (mm) cc_final: 0.8677 (tp) REVERT: D 402 ILE cc_start: 0.9084 (tp) cc_final: 0.8839 (tp) REVERT: D 472 ILE cc_start: 0.8705 (tp) cc_final: 0.8395 (tp) REVERT: D 473 TYR cc_start: 0.8965 (t80) cc_final: 0.8454 (t80) REVERT: D 516 GLU cc_start: 0.8361 (tp30) cc_final: 0.7479 (tm-30) outliers start: 2 outliers final: 0 residues processed: 126 average time/residue: 0.2057 time to fit residues: 30.1372 Evaluate side-chains 103 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.0370 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3625 Z= 0.206 Angle : 0.717 11.083 4930 Z= 0.362 Chirality : 0.047 0.175 509 Planarity : 0.005 0.047 644 Dihedral : 5.549 19.250 492 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.94 % Allowed : 12.24 % Favored : 86.82 % Rotamer: Outliers : 0.54 % Allowed : 3.22 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.38), residues: 425 helix: -2.95 (0.56), residues: 52 sheet: -0.46 (0.60), residues: 68 loop : -2.51 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 436 HIS 0.003 0.001 HIS B 519 PHE 0.017 0.002 PHE D 375 TYR 0.020 0.002 TYR B 423 ARG 0.006 0.001 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 356 LYS cc_start: 0.9409 (tppt) cc_final: 0.9172 (tppt) REVERT: B 388 ASN cc_start: 0.6847 (t0) cc_final: 0.6451 (m110) REVERT: B 403 ARG cc_start: 0.7872 (mtt180) cc_final: 0.7412 (mtt180) REVERT: D 402 ILE cc_start: 0.9193 (tp) cc_final: 0.8939 (tp) REVERT: D 462 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8841 (mtmm) REVERT: D 472 ILE cc_start: 0.8231 (tp) cc_final: 0.6939 (tp) REVERT: D 473 TYR cc_start: 0.9033 (t80) cc_final: 0.8669 (t80) REVERT: D 516 GLU cc_start: 0.8041 (tp30) cc_final: 0.7503 (tm-30) outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 0.2060 time to fit residues: 32.0532 Evaluate side-chains 91 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 0.0010 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 4.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN D 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 3625 Z= 0.387 Angle : 0.822 11.027 4930 Z= 0.428 Chirality : 0.049 0.160 509 Planarity : 0.007 0.050 644 Dihedral : 6.362 21.800 492 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.94 % Allowed : 15.53 % Favored : 83.53 % Rotamer: Outliers : 0.27 % Allowed : 4.56 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.38), residues: 425 helix: -2.71 (0.62), residues: 52 sheet: -0.86 (0.58), residues: 68 loop : -2.76 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 53 HIS 0.003 0.001 HIS B 519 PHE 0.015 0.003 PHE B 347 TYR 0.023 0.002 TYR D 501 ARG 0.005 0.001 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8354 (pm20) cc_final: 0.7197 (tp30) REVERT: A 111 ASP cc_start: 0.8565 (p0) cc_final: 0.8307 (p0) REVERT: B 356 LYS cc_start: 0.9422 (tppt) cc_final: 0.9116 (tppt) REVERT: B 403 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7583 (mtt180) REVERT: B 409 GLN cc_start: 0.9128 (mp10) cc_final: 0.8748 (mt0) REVERT: B 453 TYR cc_start: 0.8667 (t80) cc_final: 0.8095 (t80) REVERT: B 489 TYR cc_start: 0.7892 (m-80) cc_final: 0.7503 (m-80) REVERT: D 335 LEU cc_start: 0.9050 (mm) cc_final: 0.8826 (tp) REVERT: D 340 GLU cc_start: 0.9041 (mp0) cc_final: 0.8840 (mp0) REVERT: D 402 ILE cc_start: 0.9142 (tp) cc_final: 0.8911 (tp) REVERT: D 473 TYR cc_start: 0.9230 (t80) cc_final: 0.8884 (t80) REVERT: D 506 GLN cc_start: 0.8607 (mt0) cc_final: 0.8370 (mt0) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.1982 time to fit residues: 27.2776 Evaluate side-chains 89 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 0.0980 chunk 23 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3625 Z= 0.201 Angle : 0.727 11.175 4930 Z= 0.364 Chirality : 0.047 0.194 509 Planarity : 0.005 0.035 644 Dihedral : 5.890 23.520 492 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 1.18 % Allowed : 12.24 % Favored : 86.59 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.37), residues: 425 helix: -3.39 (0.56), residues: 46 sheet: -0.78 (0.58), residues: 68 loop : -2.69 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 436 HIS 0.002 0.001 HIS B 519 PHE 0.022 0.002 PHE D 400 TYR 0.017 0.002 TYR D 421 ARG 0.006 0.001 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 356 LYS cc_start: 0.9378 (tppt) cc_final: 0.9108 (tppt) REVERT: B 365 TYR cc_start: 0.8479 (m-80) cc_final: 0.7788 (m-80) REVERT: B 409 GLN cc_start: 0.9042 (mp10) cc_final: 0.8785 (mt0) REVERT: B 453 TYR cc_start: 0.8315 (t80) cc_final: 0.7922 (t80) REVERT: D 335 LEU cc_start: 0.9047 (mm) cc_final: 0.8842 (tp) REVERT: D 340 GLU cc_start: 0.9013 (mp0) cc_final: 0.8790 (mp0) REVERT: D 358 ILE cc_start: 0.8883 (mp) cc_final: 0.8661 (mp) REVERT: D 394 ASN cc_start: 0.9117 (t0) cc_final: 0.7944 (p0) REVERT: D 402 ILE cc_start: 0.9069 (tp) cc_final: 0.8756 (tp) REVERT: D 406 GLU cc_start: 0.8900 (pm20) cc_final: 0.8434 (pm20) REVERT: D 409 GLN cc_start: 0.8780 (mt0) cc_final: 0.8535 (tt0) REVERT: D 516 GLU cc_start: 0.7948 (tp30) cc_final: 0.6893 (tm-30) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1885 time to fit residues: 30.7969 Evaluate side-chains 104 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.2980 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3625 Z= 0.212 Angle : 0.731 11.033 4930 Z= 0.367 Chirality : 0.047 0.196 509 Planarity : 0.005 0.041 644 Dihedral : 5.716 19.882 492 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 1.18 % Allowed : 14.82 % Favored : 84.00 % Rotamer: Outliers : 0.27 % Allowed : 1.61 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.38), residues: 425 helix: -2.76 (0.63), residues: 47 sheet: -0.89 (0.56), residues: 74 loop : -2.66 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 436 HIS 0.002 0.001 HIS B 519 PHE 0.022 0.002 PHE D 400 TYR 0.019 0.002 TYR B 508 ARG 0.006 0.001 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8365 (pm20) cc_final: 0.7219 (tp30) REVERT: B 354 ASN cc_start: 0.9330 (t0) cc_final: 0.9088 (t0) REVERT: B 356 LYS cc_start: 0.9386 (tppt) cc_final: 0.9098 (tppt) REVERT: B 365 TYR cc_start: 0.8498 (m-80) cc_final: 0.7543 (m-80) REVERT: B 388 ASN cc_start: 0.6747 (t0) cc_final: 0.6394 (m110) REVERT: B 403 ARG cc_start: 0.7471 (mtt180) cc_final: 0.7067 (mtt90) REVERT: B 453 TYR cc_start: 0.8160 (t80) cc_final: 0.7532 (t80) REVERT: B 493 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8235 (tpp80) REVERT: D 335 LEU cc_start: 0.9044 (mm) cc_final: 0.8823 (tp) REVERT: D 340 GLU cc_start: 0.9032 (mp0) cc_final: 0.8806 (mp0) REVERT: D 358 ILE cc_start: 0.8785 (mp) cc_final: 0.8580 (mp) REVERT: D 394 ASN cc_start: 0.9061 (t0) cc_final: 0.8237 (p0) REVERT: D 402 ILE cc_start: 0.9115 (tp) cc_final: 0.8832 (tp) REVERT: D 406 GLU cc_start: 0.8946 (pm20) cc_final: 0.8467 (pm20) REVERT: D 409 GLN cc_start: 0.8822 (mt0) cc_final: 0.8529 (tt0) REVERT: D 473 TYR cc_start: 0.9228 (t80) cc_final: 0.8853 (t80) REVERT: D 478 LYS cc_start: 0.9089 (tptp) cc_final: 0.8868 (tptt) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1984 time to fit residues: 28.3820 Evaluate side-chains 99 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.0040 chunk 7 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3625 Z= 0.301 Angle : 0.779 11.408 4930 Z= 0.395 Chirality : 0.049 0.198 509 Planarity : 0.006 0.043 644 Dihedral : 6.139 22.013 492 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 1.18 % Allowed : 15.29 % Favored : 83.53 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.39), residues: 425 helix: -2.80 (0.64), residues: 47 sheet: -1.08 (0.57), residues: 74 loop : -2.70 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 436 HIS 0.002 0.001 HIS B 519 PHE 0.040 0.002 PHE B 375 TYR 0.020 0.002 TYR B 453 ARG 0.007 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8519 (pm20) cc_final: 0.7433 (tp30) REVERT: B 354 ASN cc_start: 0.9303 (t0) cc_final: 0.8987 (t0) REVERT: B 356 LYS cc_start: 0.9423 (tppt) cc_final: 0.9014 (tppt) REVERT: B 365 TYR cc_start: 0.8633 (m-80) cc_final: 0.7348 (m-80) REVERT: B 403 ARG cc_start: 0.7654 (mtt180) cc_final: 0.7380 (mpp80) REVERT: B 453 TYR cc_start: 0.8553 (t80) cc_final: 0.7805 (t80) REVERT: B 489 TYR cc_start: 0.7735 (m-80) cc_final: 0.7468 (m-80) REVERT: B 493 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8436 (tpp80) REVERT: D 335 LEU cc_start: 0.9047 (mm) cc_final: 0.8788 (tp) REVERT: D 340 GLU cc_start: 0.9049 (mp0) cc_final: 0.8832 (mp0) REVERT: D 358 ILE cc_start: 0.8776 (mp) cc_final: 0.8570 (mp) REVERT: D 394 ASN cc_start: 0.9188 (t0) cc_final: 0.8268 (p0) REVERT: D 402 ILE cc_start: 0.9073 (tp) cc_final: 0.8780 (tp) REVERT: D 406 GLU cc_start: 0.8910 (pm20) cc_final: 0.8457 (pm20) REVERT: D 473 TYR cc_start: 0.9281 (t80) cc_final: 0.9063 (t80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2167 time to fit residues: 29.4244 Evaluate side-chains 88 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 HIS D 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3625 Z= 0.193 Angle : 0.724 10.996 4930 Z= 0.366 Chirality : 0.048 0.217 509 Planarity : 0.007 0.106 644 Dihedral : 5.799 19.253 492 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 1.18 % Allowed : 13.18 % Favored : 85.65 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.38), residues: 425 helix: -3.57 (0.58), residues: 41 sheet: -0.91 (0.58), residues: 74 loop : -2.67 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 436 HIS 0.003 0.001 HIS B 505 PHE 0.018 0.002 PHE D 400 TYR 0.025 0.002 TYR B 501 ARG 0.007 0.001 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8479 (pm20) cc_final: 0.7369 (tp30) REVERT: B 354 ASN cc_start: 0.9273 (t0) cc_final: 0.8961 (t0) REVERT: B 356 LYS cc_start: 0.9388 (tppt) cc_final: 0.8979 (tppt) REVERT: B 388 ASN cc_start: 0.6841 (t0) cc_final: 0.6430 (m110) REVERT: B 403 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7398 (mtt90) REVERT: B 423 TYR cc_start: 0.8768 (t80) cc_final: 0.8429 (t80) REVERT: D 340 GLU cc_start: 0.9051 (mp0) cc_final: 0.8814 (mp0) REVERT: D 358 ILE cc_start: 0.8768 (mp) cc_final: 0.8566 (mp) REVERT: D 394 ASN cc_start: 0.9061 (t0) cc_final: 0.8289 (p0) REVERT: D 402 ILE cc_start: 0.9084 (tp) cc_final: 0.8755 (tp) REVERT: D 406 GLU cc_start: 0.8964 (pm20) cc_final: 0.8494 (pm20) REVERT: D 464 PHE cc_start: 0.8551 (m-80) cc_final: 0.8305 (m-10) REVERT: D 473 TYR cc_start: 0.9175 (t80) cc_final: 0.8890 (t80) REVERT: D 506 GLN cc_start: 0.8378 (mt0) cc_final: 0.7897 (mp10) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2036 time to fit residues: 29.8889 Evaluate side-chains 101 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 3625 Z= 0.240 Angle : 0.751 11.023 4930 Z= 0.382 Chirality : 0.047 0.218 509 Planarity : 0.006 0.086 644 Dihedral : 5.891 21.237 492 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 1.18 % Allowed : 14.82 % Favored : 84.00 % Rotamer: Outliers : 0.27 % Allowed : 0.54 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.38), residues: 425 helix: -3.24 (0.56), residues: 47 sheet: -1.04 (0.57), residues: 74 loop : -2.73 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 436 HIS 0.001 0.001 HIS D 505 PHE 0.037 0.002 PHE B 375 TYR 0.017 0.002 TYR D 421 ARG 0.008 0.001 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8549 (pm20) cc_final: 0.7429 (tp30) REVERT: B 354 ASN cc_start: 0.9289 (t0) cc_final: 0.8950 (t0) REVERT: B 356 LYS cc_start: 0.9405 (tppt) cc_final: 0.8991 (tppt) REVERT: B 388 ASN cc_start: 0.6826 (t0) cc_final: 0.6358 (m110) REVERT: B 403 ARG cc_start: 0.8094 (mtt180) cc_final: 0.6507 (mpp80) REVERT: B 423 TYR cc_start: 0.8883 (t80) cc_final: 0.8549 (t80) REVERT: C 110 ARG cc_start: 0.7614 (tpt-90) cc_final: 0.6868 (tpp-160) REVERT: D 338 PHE cc_start: 0.8822 (m-80) cc_final: 0.8531 (m-80) REVERT: D 340 GLU cc_start: 0.9064 (mp0) cc_final: 0.8811 (mp0) REVERT: D 358 ILE cc_start: 0.8768 (mp) cc_final: 0.8551 (mp) REVERT: D 394 ASN cc_start: 0.9130 (t0) cc_final: 0.8307 (p0) REVERT: D 402 ILE cc_start: 0.9083 (tp) cc_final: 0.8781 (tp) REVERT: D 406 GLU cc_start: 0.8854 (pm20) cc_final: 0.8412 (pm20) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.2071 time to fit residues: 29.4096 Evaluate side-chains 91 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3625 Z= 0.187 Angle : 0.739 13.820 4930 Z= 0.371 Chirality : 0.048 0.282 509 Planarity : 0.006 0.064 644 Dihedral : 5.722 22.874 492 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 1.18 % Allowed : 13.65 % Favored : 85.18 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.39), residues: 425 helix: -3.40 (0.62), residues: 40 sheet: -0.96 (0.58), residues: 75 loop : -2.58 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 436 HIS 0.002 0.001 HIS B 519 PHE 0.019 0.002 PHE D 400 TYR 0.017 0.002 TYR B 508 ARG 0.007 0.001 ARG B 493 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8468 (pm20) cc_final: 0.7378 (tp30) REVERT: A 111 ASP cc_start: 0.8166 (p0) cc_final: 0.7959 (p0) REVERT: B 354 ASN cc_start: 0.9261 (t0) cc_final: 0.8908 (t0) REVERT: B 356 LYS cc_start: 0.9371 (tppt) cc_final: 0.8951 (tppt) REVERT: B 388 ASN cc_start: 0.6862 (t0) cc_final: 0.6454 (m110) REVERT: B 423 TYR cc_start: 0.8892 (t80) cc_final: 0.8527 (t80) REVERT: D 338 PHE cc_start: 0.8786 (m-80) cc_final: 0.8502 (m-80) REVERT: D 340 GLU cc_start: 0.9048 (mp0) cc_final: 0.8785 (mp0) REVERT: D 358 ILE cc_start: 0.8774 (mp) cc_final: 0.8548 (mp) REVERT: D 394 ASN cc_start: 0.9014 (t0) cc_final: 0.8306 (p0) REVERT: D 402 ILE cc_start: 0.9011 (tp) cc_final: 0.8687 (tp) REVERT: D 406 GLU cc_start: 0.8880 (pm20) cc_final: 0.8436 (pm20) REVERT: D 473 TYR cc_start: 0.9186 (t80) cc_final: 0.8814 (t80) REVERT: D 506 GLN cc_start: 0.8226 (mt0) cc_final: 0.7922 (mp10) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1924 time to fit residues: 27.0908 Evaluate side-chains 94 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.0040 chunk 41 optimal weight: 6.9990 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.112045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.093289 restraints weight = 13228.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.096056 restraints weight = 8302.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.098113 restraints weight = 5842.326| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3625 Z= 0.211 Angle : 0.762 15.011 4930 Z= 0.380 Chirality : 0.049 0.314 509 Planarity : 0.006 0.058 644 Dihedral : 5.827 20.816 492 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 1.18 % Allowed : 15.06 % Favored : 83.76 % Rotamer: Outliers : 0.27 % Allowed : 0.00 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.39), residues: 425 helix: -3.45 (0.59), residues: 40 sheet: -0.92 (0.59), residues: 73 loop : -2.57 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 436 HIS 0.001 0.001 HIS B 519 PHE 0.034 0.002 PHE B 375 TYR 0.016 0.002 TYR B 421 ARG 0.007 0.001 ARG A 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1256.39 seconds wall clock time: 23 minutes 32.97 seconds (1412.97 seconds total)