Starting phenix.real_space_refine on Wed Jul 23 12:24:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c0y_16375/07_2025/8c0y_16375.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c0y_16375/07_2025/8c0y_16375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c0y_16375/07_2025/8c0y_16375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c0y_16375/07_2025/8c0y_16375.map" model { file = "/net/cci-nas-00/data/ceres_data/8c0y_16375/07_2025/8c0y_16375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c0y_16375/07_2025/8c0y_16375.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.035 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 14 5.16 5 C 2064 2.51 5 N 548 2.21 5 O 611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3237 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1530 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 11, 'TRANS': 178} Chain breaks: 1 Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "B" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 905 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Time building chain proxies: 6.32, per 1000 atoms: 1.95 Number of scatterers: 3237 At special positions: 0 Unit cell: (68.68, 70.7, 85.85, 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 14 16.00 O 611 8.00 N 548 7.00 C 2064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " 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 407.9 milliseconds 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 12.1% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.751A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.882A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 4.059A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.622A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.466A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.513A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.755A pdb=" N THR B 90 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.854A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.410A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU D 33 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N PHE D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.738A pdb=" N MET B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.962A pdb=" N CYS B 95 " --> pdb=" O TRP B 107 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TRP B 107 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG B 97 " --> pdb=" O ASP B 105 " (cutoff:3.500A) 110 hydrogen bonds defined for protein. 258 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: 0.74 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1042 1.34 - 1.46: 891 1.46 - 1.58: 1374 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3323 Sorted by residual: bond pdb=" CB PRO A 373 " pdb=" CG PRO A 373 " ideal model delta sigma weight residual 1.492 1.529 -0.037 5.00e-02 4.00e+02 5.48e-01 bond pdb=" CG1 ILE D 2 " pdb=" CD1 ILE D 2 " ideal model delta sigma weight residual 1.513 1.491 0.022 3.90e-02 6.57e+02 3.11e-01 bond pdb=" CG PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 1.503 1.484 0.019 3.40e-02 8.65e+02 2.97e-01 bond pdb=" CG PHE A 392 " pdb=" CD2 PHE A 392 " ideal model delta sigma weight residual 1.384 1.374 0.010 2.10e-02 2.27e+03 2.20e-01 bond pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " ideal model delta sigma weight residual 1.808 1.793 0.015 3.30e-02 9.18e+02 2.01e-01 ... (remaining 3318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 4332 1.08 - 2.17: 141 2.17 - 3.25: 27 3.25 - 4.34: 9 4.34 - 5.42: 2 Bond angle restraints: 4511 Sorted by residual: angle pdb=" C GLY D 50 " pdb=" N ALA D 51 " pdb=" CA ALA D 51 " ideal model delta sigma weight residual 121.54 125.74 -4.20 1.91e+00 2.74e-01 4.84e+00 angle pdb=" CB ARG D 96 " pdb=" CG ARG D 96 " pdb=" CD ARG D 96 " ideal model delta sigma weight residual 111.30 114.87 -3.57 2.30e+00 1.89e-01 2.41e+00 angle pdb=" CA TYR B 33 " pdb=" CB TYR B 33 " pdb=" CG TYR B 33 " ideal model delta sigma weight residual 113.90 116.52 -2.62 1.80e+00 3.09e-01 2.12e+00 angle pdb=" N ARG B 66 " pdb=" CA ARG B 66 " pdb=" C ARG B 66 " ideal model delta sigma weight residual 114.56 112.80 1.76 1.27e+00 6.20e-01 1.92e+00 angle pdb=" CG ARG D 96 " pdb=" CD ARG D 96 " pdb=" NE ARG D 96 " ideal model delta sigma weight residual 112.00 114.93 -2.93 2.20e+00 2.07e-01 1.77e+00 ... (remaining 4506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 1718 16.95 - 33.90: 186 33.90 - 50.84: 34 50.84 - 67.79: 6 67.79 - 84.74: 3 Dihedral angle restraints: 1947 sinusoidal: 762 harmonic: 1185 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 59.91 33.09 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CA PHE A 392 " pdb=" C PHE A 392 " pdb=" N THR A 393 " pdb=" CA THR A 393 " ideal model delta harmonic sigma weight residual 180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASP D 70 " pdb=" CB ASP D 70 " pdb=" CG ASP D 70 " pdb=" OD1 ASP D 70 " ideal model delta sinusoidal sigma weight residual -30.00 -86.50 56.50 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 1944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 249 0.026 - 0.052: 134 0.052 - 0.078: 48 0.078 - 0.104: 30 0.104 - 0.130: 13 Chirality restraints: 474 Sorted by residual: chirality pdb=" CA VAL B 2 " pdb=" N VAL B 2 " pdb=" C VAL B 2 " pdb=" CB VAL B 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE D 48 " pdb=" N ILE D 48 " pdb=" C ILE D 48 " pdb=" CB ILE D 48 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA VAL A 395 " pdb=" N VAL A 395 " pdb=" C VAL A 395 " pdb=" CB VAL A 395 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 471 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 96 " 0.298 9.50e-02 1.11e+02 1.34e-01 1.17e+01 pdb=" NE ARG D 96 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG D 96 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 96 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG D 96 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 79 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO D 80 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 346 " -0.121 9.50e-02 1.11e+02 5.45e-02 2.23e+00 pdb=" NE ARG A 346 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 346 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 346 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 346 " -0.001 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 175 2.73 - 3.27: 3021 3.27 - 3.81: 5382 3.81 - 4.36: 6655 4.36 - 4.90: 11300 Nonbonded interactions: 26533 Sorted by model distance: nonbonded pdb=" OG SER A 359 " pdb=" OD1 ASN A 394 " model vdw 2.186 3.040 nonbonded pdb=" NH1 ARG D 96 " pdb=" OD1 ASP B 101 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP A 420 " pdb=" OG SER B 56 " model vdw 2.309 3.040 nonbonded pdb=" O ASP D 82 " pdb=" OH TYR D 86 " model vdw 2.339 3.040 nonbonded pdb=" O LEU A 455 " pdb=" OH TYR B 33 " model vdw 2.340 3.040 ... (remaining 26528 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.290 Find NCS groups from input model: 0.030 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.002 0.037 3329 Z= 0.111 Angle : 0.501 5.419 4523 Z= 0.256 Chirality : 0.042 0.130 474 Planarity : 0.007 0.134 587 Dihedral : 13.890 84.738 1181 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.43), residues: 404 helix: -1.86 (1.32), residues: 13 sheet: 0.91 (0.46), residues: 134 loop : -0.43 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 107 HIS 0.001 0.000 HIS A 505 PHE 0.007 0.001 PHE A 464 TYR 0.011 0.001 TYR B 33 ARG 0.015 0.001 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.16342 ( 105) hydrogen bonds : angle 8.32941 ( 258) SS BOND : bond 0.00283 ( 6) SS BOND : angle 0.83571 ( 12) covalent geometry : bond 0.00246 ( 3323) covalent geometry : angle 0.49941 ( 4511) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.7298 (t0) cc_final: 0.7058 (t70) REVERT: A 398 ASP cc_start: 0.8075 (m-30) cc_final: 0.7781 (m-30) REVERT: A 442 ASP cc_start: 0.8997 (m-30) cc_final: 0.8785 (m-30) REVERT: A 478 LYS cc_start: 0.8988 (mmtp) cc_final: 0.8740 (mmmt) REVERT: D 2 ILE cc_start: 0.9188 (mp) cc_final: 0.8934 (mp) REVERT: B 3 HIS cc_start: 0.8637 (m90) cc_final: 0.8410 (m90) REVERT: B 26 GLU cc_start: 0.8411 (tt0) cc_final: 0.8088 (tm-30) REVERT: B 59 TYR cc_start: 0.9240 (m-80) cc_final: 0.8878 (m-80) REVERT: B 75 ARG cc_start: 0.7961 (mpp80) cc_final: 0.7514 (mpp80) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 1.4558 time to fit residues: 129.8011 Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.0270 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.0020 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 0.3246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.051895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.044881 restraints weight = 14277.260| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 4.03 r_work: 0.3057 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3329 Z= 0.146 Angle : 0.668 7.036 4523 Z= 0.336 Chirality : 0.047 0.156 474 Planarity : 0.005 0.054 587 Dihedral : 4.437 16.504 462 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.15 % Allowed : 14.66 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.42), residues: 404 helix: -4.35 (0.49), residues: 14 sheet: 1.15 (0.46), residues: 134 loop : -0.49 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 107 HIS 0.001 0.001 HIS B 3 PHE 0.011 0.001 PHE A 392 TYR 0.008 0.001 TYR B 94 ARG 0.006 0.001 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 105) hydrogen bonds : angle 6.16044 ( 258) SS BOND : bond 0.00244 ( 6) SS BOND : angle 1.23879 ( 12) covalent geometry : bond 0.00328 ( 3323) covalent geometry : angle 0.66614 ( 4511) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 THR cc_start: 0.8135 (p) cc_final: 0.7830 (t) REVERT: A 406 GLU cc_start: 0.8784 (mp0) cc_final: 0.8326 (pm20) REVERT: A 442 ASP cc_start: 0.9099 (m-30) cc_final: 0.8843 (m-30) REVERT: A 478 LYS cc_start: 0.9041 (mmtp) cc_final: 0.8804 (mmmt) REVERT: D 39 LYS cc_start: 0.9157 (tppp) cc_final: 0.8742 (mmtm) REVERT: D 42 GLN cc_start: 0.8626 (mt0) cc_final: 0.8406 (mt0) REVERT: D 79 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7799 (mm-30) REVERT: B 3 HIS cc_start: 0.8671 (m90) cc_final: 0.8376 (m90) REVERT: B 26 GLU cc_start: 0.8543 (tt0) cc_final: 0.8193 (tp30) REVERT: B 106 TYR cc_start: 0.8939 (m-80) cc_final: 0.8721 (m-80) REVERT: B 109 GLN cc_start: 0.9017 (mp10) cc_final: 0.8740 (pm20) outliers start: 4 outliers final: 0 residues processed: 66 average time/residue: 1.4342 time to fit residues: 96.9083 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 0.3980 chunk 33 optimal weight: 0.0060 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.050775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.043486 restraints weight = 14289.507| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.16 r_work: 0.3032 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3329 Z= 0.169 Angle : 0.653 9.929 4523 Z= 0.324 Chirality : 0.046 0.162 474 Planarity : 0.004 0.045 587 Dihedral : 4.364 16.869 462 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.59 % Allowed : 14.94 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.42), residues: 404 helix: -4.52 (0.45), residues: 14 sheet: 1.05 (0.46), residues: 136 loop : -0.58 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 107 HIS 0.001 0.001 HIS A 505 PHE 0.009 0.001 PHE A 392 TYR 0.009 0.001 TYR B 33 ARG 0.007 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 105) hydrogen bonds : angle 5.75563 ( 258) SS BOND : bond 0.00200 ( 6) SS BOND : angle 1.05398 ( 12) covalent geometry : bond 0.00374 ( 3323) covalent geometry : angle 0.65111 ( 4511) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 THR cc_start: 0.8168 (p) cc_final: 0.7960 (t) REVERT: A 406 GLU cc_start: 0.8912 (mp0) cc_final: 0.8466 (pm20) REVERT: A 442 ASP cc_start: 0.9140 (m-30) cc_final: 0.8867 (m-30) REVERT: A 478 LYS cc_start: 0.9018 (mmtp) cc_final: 0.8795 (mmmt) REVERT: D 42 GLN cc_start: 0.8678 (mt0) cc_final: 0.8406 (mt0) REVERT: D 79 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7936 (mm-30) REVERT: B 3 HIS cc_start: 0.8701 (m90) cc_final: 0.8435 (m90) REVERT: B 26 GLU cc_start: 0.8592 (tt0) cc_final: 0.8200 (tp30) REVERT: B 75 ARG cc_start: 0.8368 (mpp80) cc_final: 0.7907 (mpp80) REVERT: B 106 TYR cc_start: 0.8972 (m-80) cc_final: 0.8691 (m-80) outliers start: 9 outliers final: 1 residues processed: 60 average time/residue: 1.5111 time to fit residues: 92.8854 Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.0470 chunk 39 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.050598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.043472 restraints weight = 14498.817| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.07 r_work: 0.3031 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3329 Z= 0.177 Angle : 0.729 16.428 4523 Z= 0.360 Chirality : 0.046 0.161 474 Planarity : 0.004 0.041 587 Dihedral : 4.335 18.784 462 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.59 % Allowed : 16.95 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.41), residues: 404 helix: -4.47 (0.43), residues: 14 sheet: 1.01 (0.46), residues: 136 loop : -0.69 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 107 HIS 0.001 0.001 HIS A 505 PHE 0.007 0.001 PHE B 104 TYR 0.009 0.001 TYR B 33 ARG 0.008 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 105) hydrogen bonds : angle 5.68907 ( 258) SS BOND : bond 0.00364 ( 6) SS BOND : angle 2.39580 ( 12) covalent geometry : bond 0.00402 ( 3323) covalent geometry : angle 0.71991 ( 4511) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 385 THR cc_start: 0.8103 (p) cc_final: 0.7864 (t) REVERT: A 406 GLU cc_start: 0.8886 (mp0) cc_final: 0.8426 (pm20) REVERT: A 442 ASP cc_start: 0.9116 (m-30) cc_final: 0.8837 (m-30) REVERT: A 478 LYS cc_start: 0.9034 (mmtp) cc_final: 0.8825 (mmmt) REVERT: D 39 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8760 (mmtm) REVERT: D 42 GLN cc_start: 0.8686 (mt0) cc_final: 0.8447 (mt0) REVERT: D 79 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7979 (mm-30) REVERT: D 105 GLU cc_start: 0.6444 (tp30) cc_final: 0.6214 (tt0) REVERT: B 3 HIS cc_start: 0.8722 (m90) cc_final: 0.8487 (m90) REVERT: B 26 GLU cc_start: 0.8601 (tt0) cc_final: 0.8199 (tp30) REVERT: B 75 ARG cc_start: 0.8392 (mpp80) cc_final: 0.7923 (mpp80) REVERT: B 106 TYR cc_start: 0.8984 (m-80) cc_final: 0.8675 (m-80) REVERT: B 109 GLN cc_start: 0.9040 (mp10) cc_final: 0.8767 (pm20) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 1.3842 time to fit residues: 90.8921 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 39 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 0.0050 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.049069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.042031 restraints weight = 15209.816| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 4.11 r_work: 0.2985 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 3329 Z= 0.249 Angle : 0.777 14.612 4523 Z= 0.381 Chirality : 0.048 0.180 474 Planarity : 0.005 0.043 587 Dihedral : 4.623 21.430 462 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.16 % Allowed : 18.10 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.42), residues: 404 helix: -4.27 (0.56), residues: 14 sheet: 0.75 (0.43), residues: 158 loop : -0.70 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 107 HIS 0.001 0.001 HIS A 505 PHE 0.011 0.001 PHE B 104 TYR 0.011 0.001 TYR A 396 ARG 0.010 0.001 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 105) hydrogen bonds : angle 5.61416 ( 258) SS BOND : bond 0.00636 ( 6) SS BOND : angle 2.56535 ( 12) covalent geometry : bond 0.00546 ( 3323) covalent geometry : angle 0.76688 ( 4511) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 385 THR cc_start: 0.8189 (p) cc_final: 0.7923 (t) REVERT: A 406 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8412 (pm20) REVERT: A 442 ASP cc_start: 0.9222 (m-30) cc_final: 0.8958 (m-30) REVERT: A 462 LYS cc_start: 0.9200 (mppt) cc_final: 0.8818 (mppt) REVERT: A 478 LYS cc_start: 0.9028 (mmtp) cc_final: 0.8820 (mmmt) REVERT: D 42 GLN cc_start: 0.8720 (mt0) cc_final: 0.8435 (mt0) REVERT: D 79 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8038 (mm-30) REVERT: D 105 GLU cc_start: 0.6360 (tp30) cc_final: 0.6103 (tt0) REVERT: B 26 GLU cc_start: 0.8678 (tt0) cc_final: 0.8092 (tm-30) REVERT: B 75 ARG cc_start: 0.8447 (mpp80) cc_final: 0.7938 (mpp80) outliers start: 11 outliers final: 4 residues processed: 56 average time/residue: 1.6738 time to fit residues: 96.0970 Evaluate side-chains 51 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 13 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 chunk 34 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 1 optimal weight: 0.0980 overall best weight: 0.1578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 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 = 0.3366 r_free = 0.3366 target = 0.050616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.043791 restraints weight = 15074.924| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.07 r_work: 0.3044 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3329 Z= 0.124 Angle : 0.704 10.573 4523 Z= 0.348 Chirality : 0.046 0.149 474 Planarity : 0.004 0.046 587 Dihedral : 4.363 24.627 462 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.44 % Allowed : 20.69 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.42), residues: 404 helix: -4.28 (0.60), residues: 14 sheet: 1.03 (0.47), residues: 135 loop : -0.65 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS B 3 PHE 0.008 0.001 PHE A 464 TYR 0.010 0.001 TYR A 396 ARG 0.011 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.02938 ( 105) hydrogen bonds : angle 5.30283 ( 258) SS BOND : bond 0.00421 ( 6) SS BOND : angle 1.68818 ( 12) covalent geometry : bond 0.00299 ( 3323) covalent geometry : angle 0.69920 ( 4511) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 THR cc_start: 0.8144 (p) cc_final: 0.7886 (t) REVERT: A 406 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8433 (pm20) REVERT: A 424 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8530 (ttmm) REVERT: A 442 ASP cc_start: 0.9105 (m-30) cc_final: 0.8852 (m-30) REVERT: D 42 GLN cc_start: 0.8667 (mt0) cc_final: 0.8158 (mp10) REVERT: D 79 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7835 (mm-30) REVERT: D 105 GLU cc_start: 0.6406 (tp30) cc_final: 0.6131 (tt0) REVERT: B 26 GLU cc_start: 0.8562 (tt0) cc_final: 0.8189 (tp30) REVERT: B 75 ARG cc_start: 0.8462 (mpp80) cc_final: 0.7982 (mpp80) REVERT: B 106 TYR cc_start: 0.8946 (m-80) cc_final: 0.8712 (m-80) REVERT: B 109 GLN cc_start: 0.9109 (mp10) cc_final: 0.8724 (pm20) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 1.4387 time to fit residues: 82.8949 Evaluate side-chains 51 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain B residue 46 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 24 optimal weight: 0.0370 chunk 36 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.049940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.042834 restraints weight = 14592.776| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.07 r_work: 0.3015 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3329 Z= 0.176 Angle : 0.743 10.152 4523 Z= 0.367 Chirality : 0.046 0.157 474 Planarity : 0.004 0.052 587 Dihedral : 4.444 24.320 462 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.87 % Allowed : 20.98 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.42), residues: 404 helix: -4.25 (0.59), residues: 14 sheet: 1.01 (0.46), residues: 136 loop : -0.66 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 107 HIS 0.001 0.000 HIS A 505 PHE 0.008 0.001 PHE A 464 TYR 0.010 0.001 TYR B 33 ARG 0.012 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 105) hydrogen bonds : angle 5.27764 ( 258) SS BOND : bond 0.00374 ( 6) SS BOND : angle 1.56415 ( 12) covalent geometry : bond 0.00405 ( 3323) covalent geometry : angle 0.73971 ( 4511) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 THR cc_start: 0.8102 (p) cc_final: 0.7869 (t) REVERT: A 406 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8441 (pm20) REVERT: A 424 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8554 (ttmm) REVERT: A 442 ASP cc_start: 0.9183 (m-30) cc_final: 0.8954 (m-30) REVERT: D 42 GLN cc_start: 0.8698 (mt0) cc_final: 0.8448 (mp-120) REVERT: D 79 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7928 (mm-30) REVERT: D 105 GLU cc_start: 0.6309 (tp30) cc_final: 0.5993 (tt0) REVERT: B 26 GLU cc_start: 0.8613 (tt0) cc_final: 0.8195 (tp30) REVERT: B 64 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9032 (ptpp) outliers start: 10 outliers final: 3 residues processed: 55 average time/residue: 2.9705 time to fit residues: 168.1388 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain B residue 64 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.0060 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.049222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.042173 restraints weight = 14932.069| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 4.09 r_work: 0.2996 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3329 Z= 0.217 Angle : 0.776 11.922 4523 Z= 0.383 Chirality : 0.046 0.167 474 Planarity : 0.005 0.060 587 Dihedral : 4.572 22.860 462 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.87 % Allowed : 21.26 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.43), residues: 404 helix: -4.08 (0.69), residues: 14 sheet: 0.91 (0.45), residues: 147 loop : -0.65 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 107 HIS 0.001 0.001 HIS A 505 PHE 0.010 0.001 PHE A 392 TYR 0.012 0.001 TYR B 33 ARG 0.013 0.001 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 105) hydrogen bonds : angle 5.35377 ( 258) SS BOND : bond 0.00375 ( 6) SS BOND : angle 1.40296 ( 12) covalent geometry : bond 0.00487 ( 3323) covalent geometry : angle 0.77370 ( 4511) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 THR cc_start: 0.8314 (p) cc_final: 0.8041 (t) REVERT: A 406 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8480 (pm20) REVERT: A 442 ASP cc_start: 0.9215 (m-30) cc_final: 0.8989 (m-30) REVERT: D 39 LYS cc_start: 0.9192 (tppp) cc_final: 0.8941 (mmmm) REVERT: D 42 GLN cc_start: 0.8703 (mt0) cc_final: 0.8479 (mp-120) REVERT: D 79 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8027 (mm-30) REVERT: D 103 LYS cc_start: 0.9130 (tmtm) cc_final: 0.8759 (ttpp) REVERT: B 46 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8959 (pt0) REVERT: B 64 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9063 (ptpp) REVERT: B 109 GLN cc_start: 0.9115 (mp10) cc_final: 0.8829 (pm20) outliers start: 10 outliers final: 4 residues processed: 59 average time/residue: 2.1486 time to fit residues: 130.3729 Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 64 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 0.0670 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.049326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.042193 restraints weight = 14869.936| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 4.08 r_work: 0.2993 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3329 Z= 0.229 Angle : 0.824 11.913 4523 Z= 0.409 Chirality : 0.047 0.172 474 Planarity : 0.005 0.060 587 Dihedral : 4.681 23.448 462 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.59 % Allowed : 21.84 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.43), residues: 404 helix: -3.93 (0.74), residues: 14 sheet: 0.91 (0.45), residues: 147 loop : -0.64 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 107 HIS 0.001 0.001 HIS A 505 PHE 0.010 0.001 PHE A 392 TYR 0.013 0.001 TYR B 33 ARG 0.013 0.001 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03098 ( 105) hydrogen bonds : angle 5.42118 ( 258) SS BOND : bond 0.00417 ( 6) SS BOND : angle 1.26223 ( 12) covalent geometry : bond 0.00516 ( 3323) covalent geometry : angle 0.82217 ( 4511) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 THR cc_start: 0.8375 (p) cc_final: 0.8062 (t) REVERT: A 406 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8453 (pm20) REVERT: A 442 ASP cc_start: 0.9225 (m-30) cc_final: 0.8968 (m-30) REVERT: D 39 LYS cc_start: 0.9221 (tppp) cc_final: 0.8952 (mmmm) REVERT: D 42 GLN cc_start: 0.8735 (mt0) cc_final: 0.8457 (mp-120) REVERT: D 79 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7961 (mm-30) REVERT: D 103 LYS cc_start: 0.9114 (tmtm) cc_final: 0.8718 (ttpp) REVERT: B 43 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8674 (mp0) REVERT: B 46 GLN cc_start: 0.9325 (OUTLIER) cc_final: 0.9020 (pt0) REVERT: B 109 GLN cc_start: 0.9093 (mp10) cc_final: 0.8785 (pm20) outliers start: 9 outliers final: 5 residues processed: 56 average time/residue: 1.6057 time to fit residues: 92.0654 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.0170 chunk 34 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.0870 overall best weight: 0.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.050562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.043614 restraints weight = 14647.981| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 4.08 r_work: 0.3041 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3329 Z= 0.147 Angle : 0.797 9.939 4523 Z= 0.396 Chirality : 0.046 0.157 474 Planarity : 0.005 0.062 587 Dihedral : 4.531 21.829 462 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.01 % Allowed : 22.41 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.43), residues: 404 helix: -4.08 (0.65), residues: 14 sheet: 1.02 (0.48), residues: 135 loop : -0.58 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.000 0.000 HIS A 519 PHE 0.008 0.001 PHE A 392 TYR 0.010 0.001 TYR B 33 ARG 0.014 0.001 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.02919 ( 105) hydrogen bonds : angle 5.29939 ( 258) SS BOND : bond 0.00440 ( 6) SS BOND : angle 1.07638 ( 12) covalent geometry : bond 0.00361 ( 3323) covalent geometry : angle 0.79597 ( 4511) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 THR cc_start: 0.8155 (p) cc_final: 0.7892 (t) REVERT: A 406 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: A 442 ASP cc_start: 0.9131 (m-30) cc_final: 0.8899 (m-30) REVERT: D 39 LYS cc_start: 0.9185 (tppp) cc_final: 0.8968 (mmmm) REVERT: D 42 GLN cc_start: 0.8721 (mt0) cc_final: 0.8454 (mp-120) REVERT: D 79 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7912 (mm-30) REVERT: D 103 LYS cc_start: 0.9077 (tmtm) cc_final: 0.8596 (ttpp) REVERT: B 26 GLU cc_start: 0.8584 (tt0) cc_final: 0.8180 (tp30) REVERT: B 43 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8819 (mp0) REVERT: B 46 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8983 (pt0) REVERT: B 75 ARG cc_start: 0.8448 (mpp80) cc_final: 0.8010 (mpp80) REVERT: B 109 GLN cc_start: 0.9090 (mp10) cc_final: 0.8817 (pm20) outliers start: 7 outliers final: 3 residues processed: 57 average time/residue: 1.6201 time to fit residues: 94.9417 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain B residue 46 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.0670 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 18 optimal weight: 0.0980 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.050491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.043430 restraints weight = 14580.008| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 4.09 r_work: 0.3042 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3329 Z= 0.156 Angle : 0.814 9.881 4523 Z= 0.398 Chirality : 0.046 0.152 474 Planarity : 0.005 0.061 587 Dihedral : 4.536 22.511 462 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.01 % Allowed : 22.99 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.43), residues: 404 helix: -3.95 (0.70), residues: 14 sheet: 0.99 (0.48), residues: 135 loop : -0.52 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 107 HIS 0.001 0.000 HIS B 3 PHE 0.005 0.001 PHE B 104 TYR 0.012 0.001 TYR A 380 ARG 0.014 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 105) hydrogen bonds : angle 5.26260 ( 258) SS BOND : bond 0.00433 ( 6) SS BOND : angle 1.02884 ( 12) covalent geometry : bond 0.00382 ( 3323) covalent geometry : angle 0.81334 ( 4511) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4997.02 seconds wall clock time: 90 minutes 29.31 seconds (5429.31 seconds total)