Starting phenix.real_space_refine on Wed Mar 5 20:12:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jys_36730/03_2025/8jys_36730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jys_36730/03_2025/8jys_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_36730/03_2025/8jys_36730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jys_36730/03_2025/8jys_36730.map" model { file = "/net/cci-nas-00/data/ceres_data/8jys_36730/03_2025/8jys_36730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jys_36730/03_2025/8jys_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-5624/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: 2.69, per 1000 atoms: 0.76 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: 0.78 Conformation dependent library (CDL) restraints added in 418.1 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: 0.32 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: 0.72 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 0.570 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.630 Find NCS groups from input model: 0.110 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.540 ------------------------------------------------------------------------------- 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 : 0.362 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: 0.2164 time to fit residues: 26.2705 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 : 0.413 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.118320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098965 restraints weight = 12806.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.102018 restraints weight = 7888.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.104279 restraints weight = 5474.841| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 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 : 0.368 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: 0.7553 (mtt180) cc_final: 0.7288 (mtt90) REVERT: B 495 TYR cc_start: 0.6467 (m-10) cc_final: 0.6245 (m-80) REVERT: D 335 LEU cc_start: 0.8971 (mm) cc_final: 0.8678 (tp) REVERT: D 396 TYR cc_start: 0.8494 (m-80) cc_final: 0.8272 (m-80) REVERT: D 402 ILE cc_start: 0.9027 (tp) cc_final: 0.8746 (tp) REVERT: D 472 ILE cc_start: 0.8593 (tp) cc_final: 0.8297 (tp) REVERT: D 473 TYR cc_start: 0.8906 (t80) cc_final: 0.8416 (t80) REVERT: D 516 GLU cc_start: 0.8509 (tp30) cc_final: 0.7567 (tm-30) outliers start: 2 outliers final: 0 residues processed: 126 average time/residue: 0.1980 time to fit residues: 29.0720 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 : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.117620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.098278 restraints weight = 12768.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101316 restraints weight = 7809.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.103540 restraints weight = 5395.337| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3625 Z= 0.184 Angle : 0.699 10.911 4930 Z= 0.352 Chirality : 0.046 0.179 509 Planarity : 0.005 0.044 644 Dihedral : 5.454 19.273 492 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.94 % Allowed : 11.76 % Favored : 87.29 % Rotamer: Outliers : 0.27 % Allowed : 2.68 % Favored : 97.05 % 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: -3.15 (0.38), residues: 425 helix: -3.05 (0.56), residues: 52 sheet: -0.50 (0.60), residues: 69 loop : -2.49 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 HIS 0.002 0.001 HIS B 519 PHE 0.016 0.002 PHE D 400 TYR 0.020 0.001 TYR D 501 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 138 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.7316 (p0) cc_final: 0.6847 (m-30) REVERT: B 388 ASN cc_start: 0.7018 (t0) cc_final: 0.6575 (m-40) REVERT: B 403 ARG cc_start: 0.7452 (mtt180) cc_final: 0.7018 (mtt90) REVERT: B 471 GLU cc_start: 0.9089 (tp30) cc_final: 0.8826 (tp30) REVERT: B 495 TYR cc_start: 0.6486 (m-10) cc_final: 0.6220 (m-80) REVERT: D 335 LEU cc_start: 0.8939 (mm) cc_final: 0.8660 (tp) REVERT: D 394 ASN cc_start: 0.9222 (t0) cc_final: 0.8368 (p0) REVERT: D 402 ILE cc_start: 0.9098 (tp) cc_final: 0.8857 (tp) REVERT: D 425 LEU cc_start: 0.9049 (pp) cc_final: 0.8837 (pp) REVERT: D 462 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8839 (mtmm) REVERT: D 473 TYR cc_start: 0.8868 (t80) cc_final: 0.8556 (t80) REVERT: D 516 GLU cc_start: 0.8395 (tp30) cc_final: 0.7570 (tm-30) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.2155 time to fit residues: 34.4151 Evaluate side-chains 105 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.112991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.093709 restraints weight = 13598.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.096574 restraints weight = 8530.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.098616 restraints weight = 6006.620| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3625 Z= 0.230 Angle : 0.713 10.723 4930 Z= 0.364 Chirality : 0.047 0.174 509 Planarity : 0.005 0.045 644 Dihedral : 5.531 18.371 492 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.94 % Allowed : 12.00 % Favored : 87.06 % Rotamer: Outliers : 0.27 % Allowed : 3.22 % Favored : 96.51 % 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: -3.17 (0.38), residues: 425 helix: -2.90 (0.57), residues: 52 sheet: -0.56 (0.60), residues: 68 loop : -2.52 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 53 HIS 0.002 0.001 HIS B 519 PHE 0.018 0.002 PHE B 456 TYR 0.018 0.002 TYR B 423 ARG 0.006 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 129 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 356 LYS cc_start: 0.9427 (tppt) cc_final: 0.9218 (tppt) REVERT: B 388 ASN cc_start: 0.6922 (t0) cc_final: 0.6489 (m110) REVERT: B 453 TYR cc_start: 0.8436 (t80) cc_final: 0.8019 (t80) REVERT: B 471 GLU cc_start: 0.9107 (tp30) cc_final: 0.8894 (tp30) REVERT: D 340 GLU cc_start: 0.9104 (mp0) cc_final: 0.8875 (mp0) REVERT: D 386 LYS cc_start: 0.8626 (pttt) cc_final: 0.8367 (pttp) REVERT: D 394 ASN cc_start: 0.9319 (t0) cc_final: 0.8272 (p0) REVERT: D 402 ILE cc_start: 0.9137 (tp) cc_final: 0.8848 (tp) REVERT: D 406 GLU cc_start: 0.9020 (pm20) cc_final: 0.8598 (pm20) REVERT: D 409 GLN cc_start: 0.8831 (mt0) cc_final: 0.8501 (tt0) REVERT: D 424 LYS cc_start: 0.9043 (pptt) cc_final: 0.8708 (pptt) REVERT: D 425 LEU cc_start: 0.9134 (pp) cc_final: 0.8703 (pp) REVERT: D 473 TYR cc_start: 0.8855 (t80) cc_final: 0.8482 (t80) REVERT: D 486 PHE cc_start: 0.7530 (t80) cc_final: 0.7166 (t80) REVERT: D 516 GLU cc_start: 0.8416 (tp30) cc_final: 0.7405 (tm-30) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.2008 time to fit residues: 30.0415 Evaluate side-chains 96 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.107334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.088034 restraints weight = 13580.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.090863 restraints weight = 8512.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092892 restraints weight = 5992.826| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3625 Z= 0.319 Angle : 0.777 12.059 4930 Z= 0.403 Chirality : 0.049 0.184 509 Planarity : 0.006 0.040 644 Dihedral : 6.125 20.722 492 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 1.18 % Allowed : 13.41 % Favored : 85.41 % Rotamer: Outliers : 0.27 % Allowed : 4.29 % Favored : 95.44 % 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 (0.38), residues: 425 helix: -2.69 (0.61), residues: 53 sheet: -1.07 (0.56), residues: 69 loop : -2.69 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 436 HIS 0.003 0.001 HIS B 519 PHE 0.041 0.003 PHE B 375 TYR 0.021 0.002 TYR B 508 ARG 0.007 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 116 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.403 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: 0.8359 (pm20) cc_final: 0.7175 (tp30) REVERT: A 111 ASP cc_start: 0.8431 (p0) cc_final: 0.8216 (p0) REVERT: B 356 LYS cc_start: 0.9428 (tppt) cc_final: 0.9145 (tppt) REVERT: B 409 GLN cc_start: 0.9063 (mp10) cc_final: 0.8688 (mt0) REVERT: B 423 TYR cc_start: 0.8917 (t80) cc_final: 0.8544 (t80) REVERT: B 489 TYR cc_start: 0.7712 (m-80) cc_final: 0.7450 (m-80) REVERT: D 335 LEU cc_start: 0.9140 (mm) cc_final: 0.8925 (tp) REVERT: D 340 GLU cc_start: 0.9121 (mp0) cc_final: 0.8883 (mp0) REVERT: D 396 TYR cc_start: 0.8739 (m-80) cc_final: 0.8351 (m-80) REVERT: D 402 ILE cc_start: 0.9173 (tp) cc_final: 0.8836 (tp) REVERT: D 406 GLU cc_start: 0.8947 (pm20) cc_final: 0.8623 (pm20) REVERT: D 472 ILE cc_start: 0.7694 (tp) cc_final: 0.6377 (tp) REVERT: D 473 TYR cc_start: 0.8932 (t80) cc_final: 0.8575 (t80) REVERT: D 506 GLN cc_start: 0.8575 (mt0) cc_final: 0.8312 (mt0) REVERT: D 516 GLU cc_start: 0.8382 (tp30) cc_final: 0.7874 (tm-30) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.1944 time to fit residues: 26.2912 Evaluate side-chains 92 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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: 0.8980 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN B 481 ASN D 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.110669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.091872 restraints weight = 13654.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.094706 restraints weight = 8370.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096779 restraints weight = 5824.562| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.5269 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= 0.220 Angle : 0.734 11.635 4930 Z= 0.370 Chirality : 0.047 0.189 509 Planarity : 0.005 0.042 644 Dihedral : 5.829 20.992 492 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 1.18 % Allowed : 12.71 % Favored : 86.12 % Rotamer: Outliers : 0.54 % Allowed : 2.41 % Favored : 97.05 % 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: -3.27 (0.38), residues: 425 helix: -3.16 (0.59), residues: 47 sheet: -0.71 (0.58), residues: 73 loop : -2.58 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 436 HIS 0.001 0.001 HIS D 519 PHE 0.022 0.002 PHE D 400 TYR 0.017 0.002 TYR B 508 ARG 0.007 0.001 ARG A 110 *********************** 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 128 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.406 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: 0.8354 (pm20) cc_final: 0.7214 (tp30) REVERT: B 354 ASN cc_start: 0.9357 (t0) cc_final: 0.9106 (t0) REVERT: B 356 LYS cc_start: 0.9400 (tppt) cc_final: 0.9124 (tppt) REVERT: B 365 TYR cc_start: 0.8571 (m-80) cc_final: 0.7439 (m-80) REVERT: B 403 ARG cc_start: 0.8095 (mtt180) cc_final: 0.7660 (mpp80) REVERT: B 409 GLN cc_start: 0.9080 (mp10) cc_final: 0.8873 (mt0) REVERT: B 453 TYR cc_start: 0.8636 (t80) cc_final: 0.8306 (t80) REVERT: D 335 LEU cc_start: 0.9099 (mm) cc_final: 0.8885 (tp) REVERT: D 340 GLU cc_start: 0.9077 (mp0) cc_final: 0.8821 (mp0) REVERT: D 358 ILE cc_start: 0.8899 (mp) cc_final: 0.8675 (mp) REVERT: D 394 ASN cc_start: 0.9234 (t0) cc_final: 0.7988 (p0) REVERT: D 396 TYR cc_start: 0.8622 (m-80) cc_final: 0.8038 (m-80) REVERT: D 402 ILE cc_start: 0.9079 (tp) cc_final: 0.8738 (tp) REVERT: D 406 GLU cc_start: 0.8970 (pm20) cc_final: 0.8622 (pm20) REVERT: D 486 PHE cc_start: 0.7758 (t80) cc_final: 0.7369 (t80) REVERT: D 516 GLU cc_start: 0.8309 (tp30) cc_final: 0.7328 (tm-30) outliers start: 2 outliers final: 0 residues processed: 128 average time/residue: 0.1942 time to fit residues: 29.1254 Evaluate side-chains 98 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.0370 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.114019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.094998 restraints weight = 13225.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.097959 restraints weight = 8191.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.100019 restraints weight = 5711.612| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3625 Z= 0.182 Angle : 0.732 11.240 4930 Z= 0.367 Chirality : 0.047 0.234 509 Planarity : 0.005 0.042 644 Dihedral : 5.601 18.960 492 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 1.18 % Allowed : 12.94 % Favored : 85.88 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.21 (0.38), residues: 425 helix: -3.37 (0.60), residues: 41 sheet: -0.89 (0.57), residues: 75 loop : -2.47 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 436 HIS 0.003 0.001 HIS B 505 PHE 0.034 0.002 PHE B 375 TYR 0.016 0.001 TYR D 421 ARG 0.007 0.001 ARG B 493 *********************** 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 130 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.364 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: A 57 GLU cc_start: 0.8387 (pm20) cc_final: 0.7247 (tp30) REVERT: B 354 ASN cc_start: 0.9320 (t0) cc_final: 0.9119 (t0) REVERT: B 356 LYS cc_start: 0.9396 (tppt) cc_final: 0.9120 (tppt) REVERT: B 388 ASN cc_start: 0.6782 (t0) cc_final: 0.6388 (m110) REVERT: B 403 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7905 (mtt90) REVERT: B 453 TYR cc_start: 0.8645 (t80) cc_final: 0.7874 (t80) REVERT: D 335 LEU cc_start: 0.9080 (mm) cc_final: 0.8867 (tp) REVERT: D 340 GLU cc_start: 0.9083 (mp0) cc_final: 0.8814 (mp0) REVERT: D 355 ARG cc_start: 0.9115 (tpp80) cc_final: 0.8102 (tpp80) REVERT: D 394 ASN cc_start: 0.9243 (t0) cc_final: 0.8389 (p0) REVERT: D 396 TYR cc_start: 0.8615 (m-80) cc_final: 0.7896 (m-80) REVERT: D 402 ILE cc_start: 0.9086 (tp) cc_final: 0.8729 (tp) REVERT: D 406 GLU cc_start: 0.9022 (pm20) cc_final: 0.8408 (pm20) REVERT: D 409 GLN cc_start: 0.8807 (mt0) cc_final: 0.8535 (tt0) REVERT: D 473 TYR cc_start: 0.9124 (t80) cc_final: 0.8733 (t80) REVERT: D 486 PHE cc_start: 0.7834 (t80) cc_final: 0.7328 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1913 time to fit residues: 29.0814 Evaluate side-chains 100 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** 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 = 0.3719 r_free = 0.3719 target = 0.113331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.094654 restraints weight = 13604.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.097438 restraints weight = 8440.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.099487 restraints weight = 5907.207| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3625 Z= 0.193 Angle : 0.720 11.337 4930 Z= 0.362 Chirality : 0.047 0.206 509 Planarity : 0.005 0.050 644 Dihedral : 5.594 19.860 492 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.61 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: -3.10 (0.39), residues: 425 helix: -2.48 (0.71), residues: 41 sheet: -1.08 (0.57), residues: 75 loop : -2.43 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 436 HIS 0.003 0.001 HIS B 519 PHE 0.019 0.002 PHE D 400 TYR 0.019 0.001 TYR B 508 ARG 0.006 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 125 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.403 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: 0.8426 (pm20) cc_final: 0.7318 (tp30) REVERT: B 354 ASN cc_start: 0.9305 (t0) cc_final: 0.9062 (t0) REVERT: B 356 LYS cc_start: 0.9412 (tppt) cc_final: 0.9095 (tppt) REVERT: B 388 ASN cc_start: 0.6829 (t0) cc_final: 0.6438 (m110) REVERT: B 402 ILE cc_start: 0.8235 (mp) cc_final: 0.7993 (mp) REVERT: B 403 ARG cc_start: 0.8324 (mtt180) cc_final: 0.7724 (mtt90) REVERT: B 453 TYR cc_start: 0.8521 (t80) cc_final: 0.7125 (t80) REVERT: D 335 LEU cc_start: 0.9058 (mm) cc_final: 0.8829 (tp) REVERT: D 340 GLU cc_start: 0.9102 (mp0) cc_final: 0.8826 (mp0) REVERT: D 394 ASN cc_start: 0.9194 (t0) cc_final: 0.8344 (p0) REVERT: D 396 TYR cc_start: 0.8553 (m-80) cc_final: 0.8008 (m-80) REVERT: D 402 ILE cc_start: 0.9060 (tp) cc_final: 0.8717 (tp) REVERT: D 406 GLU cc_start: 0.9005 (pm20) cc_final: 0.8622 (pm20) REVERT: D 409 GLN cc_start: 0.8829 (mt0) cc_final: 0.8516 (tt0) REVERT: D 473 TYR cc_start: 0.9119 (t80) cc_final: 0.8712 (t80) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1935 time to fit residues: 28.2674 Evaluate side-chains 92 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 33 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.113656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.094778 restraints weight = 13368.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.097578 restraints weight = 8362.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.099568 restraints weight = 5886.373| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3625 Z= 0.217 Angle : 0.758 11.469 4930 Z= 0.381 Chirality : 0.047 0.221 509 Planarity : 0.008 0.139 644 Dihedral : 5.786 22.754 492 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 1.18 % Allowed : 13.18 % Favored : 85.65 % Rotamer: Outliers : 0.27 % Allowed : 0.27 % 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: -3.02 (0.39), residues: 425 helix: -2.41 (0.73), residues: 41 sheet: -0.94 (0.60), residues: 70 loop : -2.39 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 436 HIS 0.002 0.000 HIS B 519 PHE 0.035 0.002 PHE D 429 TYR 0.016 0.002 TYR B 501 ARG 0.007 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 119 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 ASN cc_start: 0.9345 (t0) cc_final: 0.9051 (t0) REVERT: B 356 LYS cc_start: 0.9392 (tppt) cc_final: 0.9092 (tppt) REVERT: B 388 ASN cc_start: 0.6903 (t0) cc_final: 0.6502 (m110) REVERT: B 403 ARG cc_start: 0.8301 (mtt180) cc_final: 0.7734 (mtt90) REVERT: B 453 TYR cc_start: 0.8693 (t80) cc_final: 0.7704 (t80) REVERT: B 493 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.8273 (tpp80) REVERT: D 335 LEU cc_start: 0.9086 (mm) cc_final: 0.8853 (tp) REVERT: D 340 GLU cc_start: 0.9143 (mp0) cc_final: 0.8854 (mp0) REVERT: D 394 ASN cc_start: 0.9301 (t0) cc_final: 0.8395 (p0) REVERT: D 396 TYR cc_start: 0.8683 (m-80) cc_final: 0.8098 (m-80) REVERT: D 402 ILE cc_start: 0.9085 (tp) cc_final: 0.8719 (tp) REVERT: D 406 GLU cc_start: 0.8974 (pm20) cc_final: 0.8606 (pm20) REVERT: D 409 GLN cc_start: 0.8899 (mt0) cc_final: 0.8567 (tt0) REVERT: D 439 ASN cc_start: 0.8995 (p0) cc_final: 0.8745 (m110) REVERT: D 473 TYR cc_start: 0.9032 (t80) cc_final: 0.8725 (t80) REVERT: D 506 GLN cc_start: 0.8408 (mt0) cc_final: 0.8073 (mt0) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.1906 time to fit residues: 26.5932 Evaluate side-chains 87 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.0000 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 0.0020 chunk 33 optimal weight: 10.0000 chunk 4 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN B 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.119194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.100183 restraints weight = 13384.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.103080 restraints weight = 8354.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.105162 restraints weight = 5852.796| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3625 Z= 0.184 Angle : 0.764 13.979 4930 Z= 0.377 Chirality : 0.049 0.284 509 Planarity : 0.006 0.052 644 Dihedral : 5.425 20.388 492 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 1.18 % Allowed : 13.18 % Favored : 85.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.99 (0.39), residues: 425 helix: -2.80 (0.66), residues: 41 sheet: -0.71 (0.59), residues: 75 loop : -2.39 (0.35), residues: 309 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 0.028 0.002 PHE D 429 TYR 0.017 0.001 TYR B 508 ARG 0.008 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 118 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.404 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: 0.8382 (pm20) cc_final: 0.7216 (tp30) REVERT: B 354 ASN cc_start: 0.9313 (t0) cc_final: 0.9064 (t0) REVERT: B 356 LYS cc_start: 0.9377 (tppt) cc_final: 0.9119 (tppt) REVERT: B 388 ASN cc_start: 0.7051 (t0) cc_final: 0.6589 (m-40) REVERT: B 453 TYR cc_start: 0.8247 (t80) cc_final: 0.7814 (t80) REVERT: B 477 ASN cc_start: 0.9187 (m110) cc_final: 0.8930 (m-40) REVERT: B 493 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8057 (tpp80) REVERT: D 335 LEU cc_start: 0.9069 (mm) cc_final: 0.8842 (tp) REVERT: D 340 GLU cc_start: 0.9179 (mp0) cc_final: 0.8854 (mp0) REVERT: D 394 ASN cc_start: 0.9263 (t0) cc_final: 0.8421 (p0) REVERT: D 396 TYR cc_start: 0.8609 (m-80) cc_final: 0.8087 (m-80) REVERT: D 402 ILE cc_start: 0.8969 (tp) cc_final: 0.8480 (tp) REVERT: D 406 GLU cc_start: 0.9011 (pm20) cc_final: 0.8666 (pm20) REVERT: D 409 GLN cc_start: 0.8954 (mt0) cc_final: 0.8695 (tt0) REVERT: D 473 TYR cc_start: 0.8889 (t80) cc_final: 0.8572 (t80) REVERT: D 486 PHE cc_start: 0.7466 (t80) cc_final: 0.6798 (t80) REVERT: D 516 GLU cc_start: 0.8384 (tp30) cc_final: 0.7479 (tp30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1980 time to fit residues: 27.4440 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.109355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091280 restraints weight = 13810.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.093948 restraints weight = 8576.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.095867 restraints weight = 6041.433| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3625 Z= 0.287 Angle : 0.793 11.106 4930 Z= 0.404 Chirality : 0.050 0.237 509 Planarity : 0.007 0.095 644 Dihedral : 5.750 20.697 492 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 1.18 % Allowed : 15.53 % Favored : 83.29 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % 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: -3.20 (0.39), residues: 425 helix: -3.04 (0.60), residues: 47 sheet: -0.97 (0.58), residues: 75 loop : -2.46 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 436 HIS 0.002 0.001 HIS D 519 PHE 0.029 0.002 PHE B 456 TYR 0.019 0.002 TYR B 508 ARG 0.008 0.001 ARG A 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1610.94 seconds wall clock time: 28 minutes 39.23 seconds (1719.23 seconds total)