Starting phenix.real_space_refine on Wed Mar 5 17:40:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xh8_33191/03_2025/7xh8_33191.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xh8_33191/03_2025/7xh8_33191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xh8_33191/03_2025/7xh8_33191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xh8_33191/03_2025/7xh8_33191.map" model { file = "/net/cci-nas-00/data/ceres_data/7xh8_33191/03_2025/7xh8_33191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xh8_33191/03_2025/7xh8_33191.cif" } resolution = 2.99 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= -0.001 sd= 0.027 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 2010 2.51 5 N 542 2.21 5 O 593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 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: 3161 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1422 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 167} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 97} Time building chain proxies: 3.01, per 1000 atoms: 0.95 Number of scatterers: 3161 At special positions: 0 Unit cell: (53, 71.02, 100.7, 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 593 8.00 N 542 7.00 C 2010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 377.1 milliseconds 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 9 sheets defined 14.9% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.096A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.025A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.650A 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 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.888A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 359 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.598A pdb=" N GLU B 10 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET B 35 " --> pdb=" O TRP B 51 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP B 51 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TRP B 37 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.598A pdb=" N GLU B 10 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.546A pdb=" N ILE B 106 " --> pdb=" O SER B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.526A pdb=" N ASP C 71 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.884A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) 118 hydrogen bonds defined for protein. 267 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: 0.86 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 697 1.33 - 1.45: 771 1.45 - 1.58: 1752 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3240 Sorted by residual: bond pdb=" N GLN C 90 " pdb=" CA GLN C 90 " ideal model delta sigma weight residual 1.458 1.512 -0.055 1.16e-02 7.43e+03 2.21e+01 bond pdb=" N GLN C 91 " pdb=" CA GLN C 91 " ideal model delta sigma weight residual 1.454 1.503 -0.049 1.21e-02 6.83e+03 1.65e+01 bond pdb=" N CYS B 102 " pdb=" CA CYS B 102 " ideal model delta sigma weight residual 1.454 1.498 -0.044 1.16e-02 7.43e+03 1.45e+01 bond pdb=" NE ARG B 68 " pdb=" CZ ARG B 68 " ideal model delta sigma weight residual 1.326 1.367 -0.041 1.10e-02 8.26e+03 1.37e+01 bond pdb=" N TYR C 92 " pdb=" CA TYR C 92 " ideal model delta sigma weight residual 1.455 1.502 -0.047 1.32e-02 5.74e+03 1.29e+01 ... (remaining 3235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 2652 1.44 - 2.88: 1234 2.88 - 4.32: 426 4.32 - 5.76: 73 5.76 - 7.20: 16 Bond angle restraints: 4401 Sorted by residual: angle pdb=" OE1 GLN B 3 " pdb=" CD GLN B 3 " pdb=" NE2 GLN B 3 " ideal model delta sigma weight residual 122.60 117.45 5.15 1.00e+00 1.00e+00 2.66e+01 angle pdb=" OD1 ASN B 58 " pdb=" CG ASN B 58 " pdb=" ND2 ASN B 58 " ideal model delta sigma weight residual 122.60 117.46 5.14 1.00e+00 1.00e+00 2.64e+01 angle pdb=" CA PRO A 373 " pdb=" N PRO A 373 " pdb=" CD PRO A 373 " ideal model delta sigma weight residual 112.00 105.22 6.78 1.40e+00 5.10e-01 2.34e+01 angle pdb=" CA ASP A 339 " pdb=" CB ASP A 339 " pdb=" CG ASP A 339 " ideal model delta sigma weight residual 112.60 107.82 4.78 1.00e+00 1.00e+00 2.28e+01 angle pdb=" C SER C 77 " pdb=" N ARG C 78 " pdb=" CA ARG C 78 " ideal model delta sigma weight residual 121.76 128.96 -7.20 1.51e+00 4.39e-01 2.27e+01 ... (remaining 4396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 1834 23.67 - 47.34: 59 47.34 - 71.01: 10 71.01 - 94.68: 4 94.68 - 118.34: 1 Dihedral angle restraints: 1908 sinusoidal: 735 harmonic: 1173 Sorted by residual: dihedral pdb=" CA ALA A 372 " pdb=" C ALA A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual 180.00 61.66 118.34 0 5.00e+00 4.00e-02 5.60e+02 dihedral pdb=" CA TYR B 96 " pdb=" C TYR B 96 " pdb=" N CYS B 97 " pdb=" CA CYS B 97 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA SER C 95 " pdb=" C SER C 95 " pdb=" N PRO C 96 " pdb=" CA PRO C 96 " ideal model delta harmonic sigma weight residual 0.00 -27.70 27.70 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 1905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 214 0.057 - 0.114: 159 0.114 - 0.170: 77 0.170 - 0.227: 22 0.227 - 0.284: 5 Chirality restraints: 477 Sorted by residual: chirality pdb=" CA ALA C 52 " pdb=" N ALA C 52 " pdb=" C ALA C 52 " pdb=" CB ALA C 52 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA SER A 514 " pdb=" N SER A 514 " pdb=" C SER A 514 " pdb=" CB SER A 514 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ASP B 109 " pdb=" N ASP B 109 " pdb=" C ASP B 109 " pdb=" CB ASP B 109 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 474 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 453 " -0.145 2.00e-02 2.50e+03 8.47e-02 1.43e+02 pdb=" CG TYR A 453 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 453 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 453 " 0.080 2.00e-02 2.50e+03 pdb=" CE1 TYR A 453 " 0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR A 453 " 0.050 2.00e-02 2.50e+03 pdb=" CZ TYR A 453 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR A 453 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 489 " 0.136 2.00e-02 2.50e+03 8.39e-02 1.41e+02 pdb=" CG TYR A 489 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 489 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TYR A 489 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR A 489 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR A 489 " -0.079 2.00e-02 2.50e+03 pdb=" CZ TYR A 489 " -0.023 2.00e-02 2.50e+03 pdb=" OH TYR A 489 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 97 " 0.134 2.00e-02 2.50e+03 7.32e-02 1.34e+02 pdb=" CG TRP C 97 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP C 97 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 97 " -0.081 2.00e-02 2.50e+03 pdb=" NE1 TRP C 97 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP C 97 " -0.030 2.00e-02 2.50e+03 pdb=" CE3 TRP C 97 " -0.103 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 97 " 0.066 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 97 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP C 97 " 0.105 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 1360 2.96 - 3.44: 2801 3.44 - 3.93: 5495 3.93 - 4.41: 5951 4.41 - 4.90: 9884 Nonbonded interactions: 25491 Sorted by model distance: nonbonded pdb=" OE1 GLN C 90 " pdb=" OH TYR C 92 " model vdw 2.472 3.040 nonbonded pdb=" OG1 THR C 70 " pdb=" OD1 ASP C 71 " model vdw 2.533 3.040 nonbonded pdb=" OD2 ASP B 74 " pdb=" OG1 THR B 77 " model vdw 2.544 3.040 nonbonded pdb=" OD1 ASP A 467 " pdb=" OG SER A 469 " model vdw 2.573 3.040 nonbonded pdb=" OE1 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.576 3.120 ... (remaining 25486 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: 2.070 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.980 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 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 : 0.014 0.062 3240 Z= 0.938 Angle : 1.807 7.196 4401 Z= 1.188 Chirality : 0.092 0.284 477 Planarity : 0.028 0.167 567 Dihedral : 13.607 118.345 1158 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 1.01 % Allowed : 3.52 % Favored : 95.48 % Rotamer: Outliers : 0.88 % Allowed : 3.80 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.88 (0.37), residues: 398 helix: -4.13 (0.47), residues: 34 sheet: -0.90 (0.43), residues: 125 loop : -0.94 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.134 0.031 TRP C 97 HIS 0.009 0.006 HIS A 505 PHE 0.087 0.017 PHE B 111 TYR 0.148 0.027 TYR A 489 ARG 0.018 0.003 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 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: symmetry clash REVERT: B 81 TYR cc_start: 0.7399 (m-80) cc_final: 0.6943 (m-80) outliers start: 3 outliers final: 0 residues processed: 120 average time/residue: 1.3191 time to fit residues: 162.0172 Evaluate side-chains 38 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS C 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.078097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.071591 restraints weight = 17733.714| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 4.61 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3240 Z= 0.266 Angle : 0.793 10.763 4401 Z= 0.399 Chirality : 0.047 0.152 477 Planarity : 0.006 0.053 567 Dihedral : 5.991 46.428 448 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.63 % Allowed : 17.84 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.19 (0.39), residues: 398 helix: -3.05 (0.71), residues: 33 sheet: -0.66 (0.40), residues: 144 loop : -0.38 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 37 HIS 0.001 0.001 HIS A 505 PHE 0.013 0.002 PHE C 99 TYR 0.016 0.002 TYR A 495 ARG 0.009 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TRP cc_start: 0.7426 (m100) cc_final: 0.7159 (m100) REVERT: B 109 ASP cc_start: 0.7339 (m-30) cc_final: 0.7059 (t70) outliers start: 9 outliers final: 5 residues processed: 66 average time/residue: 1.0011 time to fit residues: 68.3445 Evaluate side-chains 51 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.0020 chunk 25 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.073604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.066886 restraints weight = 18075.354| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 4.39 r_work: 0.3841 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3240 Z= 0.275 Angle : 0.746 10.659 4401 Z= 0.372 Chirality : 0.045 0.134 477 Planarity : 0.006 0.060 567 Dihedral : 5.653 38.480 448 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.63 % Allowed : 16.67 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.93 (0.41), residues: 398 helix: -3.39 (0.60), residues: 31 sheet: -0.42 (0.43), residues: 137 loop : -0.21 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 36 HIS 0.001 0.000 HIS A 505 PHE 0.013 0.002 PHE B 65 TYR 0.017 0.002 TYR A 495 ARG 0.014 0.001 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.8191 (pm20) cc_final: 0.7687 (pp20) REVERT: B 64 LYS cc_start: 0.9434 (tppt) cc_final: 0.9183 (tppt) REVERT: B 109 ASP cc_start: 0.7783 (m-30) cc_final: 0.7330 (OUTLIER) REVERT: B 114 TRP cc_start: 0.8361 (m-10) cc_final: 0.7965 (m-10) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 1.0765 time to fit residues: 61.2756 Evaluate side-chains 41 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 38 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.072084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.065448 restraints weight = 18572.341| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 4.45 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.7171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3240 Z= 0.224 Angle : 0.717 11.511 4401 Z= 0.346 Chirality : 0.045 0.158 477 Planarity : 0.005 0.047 567 Dihedral : 5.142 31.812 448 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.68 % Allowed : 17.25 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.94 (0.41), residues: 398 helix: -3.33 (0.67), residues: 31 sheet: -0.33 (0.43), residues: 138 loop : -0.31 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 114 HIS 0.001 0.001 HIS A 505 PHE 0.009 0.001 PHE B 65 TYR 0.015 0.001 TYR A 495 ARG 0.004 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: B 4 LEU cc_start: 0.7991 (mt) cc_final: 0.7323 (tp) REVERT: B 38 VAL cc_start: 0.8751 (t) cc_final: 0.8457 (p) REVERT: B 52 ILE cc_start: 0.8949 (tt) cc_final: 0.8689 (tp) REVERT: C 37 PHE cc_start: 0.7366 (m-80) cc_final: 0.6992 (m-80) outliers start: 16 outliers final: 9 residues processed: 52 average time/residue: 0.8621 time to fit residues: 46.8117 Evaluate side-chains 42 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.066691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.060283 restraints weight = 19155.138| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 4.26 r_work: 0.3674 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.8784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 3240 Z= 0.541 Angle : 0.974 13.332 4401 Z= 0.495 Chirality : 0.052 0.221 477 Planarity : 0.007 0.069 567 Dihedral : 6.848 27.079 448 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 24.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.68 % Allowed : 19.30 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.80 (0.40), residues: 398 helix: -4.49 (0.58), residues: 27 sheet: -0.44 (0.44), residues: 133 loop : -1.23 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP B 114 HIS 0.003 0.002 HIS A 505 PHE 0.022 0.003 PHE B 65 TYR 0.034 0.003 TYR A 369 ARG 0.016 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 VAL cc_start: 0.8859 (t) cc_final: 0.8190 (p) REVERT: B 46 LEU cc_start: 0.8771 (mm) cc_final: 0.8408 (tp) REVERT: B 109 ASP cc_start: 0.7879 (m-30) cc_final: 0.7173 (t70) REVERT: C 17 GLU cc_start: 0.7916 (tp30) cc_final: 0.7712 (mm-30) outliers start: 16 outliers final: 8 residues processed: 51 average time/residue: 0.9473 time to fit residues: 50.2023 Evaluate side-chains 39 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.069997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.063315 restraints weight = 19608.280| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 4.61 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.8627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3240 Z= 0.198 Angle : 0.772 13.014 4401 Z= 0.370 Chirality : 0.046 0.172 477 Planarity : 0.005 0.050 567 Dihedral : 5.156 22.517 448 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.22 % Allowed : 21.93 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.25 (0.41), residues: 398 helix: -4.41 (0.52), residues: 27 sheet: -0.24 (0.45), residues: 134 loop : -0.68 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 114 HIS 0.001 0.000 HIS A 505 PHE 0.022 0.002 PHE B 65 TYR 0.015 0.001 TYR A 495 ARG 0.011 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 VAL cc_start: 0.8815 (t) cc_final: 0.8214 (p) REVERT: B 46 LEU cc_start: 0.8673 (mm) cc_final: 0.8347 (tp) REVERT: B 75 MET cc_start: 0.8678 (mmp) cc_final: 0.8443 (mmp) REVERT: B 106 ILE cc_start: 0.8504 (mp) cc_final: 0.8038 (tp) REVERT: B 109 ASP cc_start: 0.7564 (m-30) cc_final: 0.6985 (OUTLIER) REVERT: B 114 TRP cc_start: 0.7930 (m-10) cc_final: 0.7709 (m-10) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.8283 time to fit residues: 40.7112 Evaluate side-chains 42 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 14 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.069904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.063096 restraints weight = 18117.253| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 4.51 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.8723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3240 Z= 0.178 Angle : 0.726 12.748 4401 Z= 0.345 Chirality : 0.045 0.155 477 Planarity : 0.005 0.049 567 Dihedral : 4.554 18.459 448 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.05 % Allowed : 22.22 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.71 (0.43), residues: 398 helix: -4.33 (0.50), residues: 25 sheet: -0.02 (0.45), residues: 136 loop : -0.20 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 114 HIS 0.000 0.000 HIS A 505 PHE 0.017 0.001 PHE B 65 TYR 0.013 0.001 TYR A 495 ARG 0.009 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 VAL cc_start: 0.8838 (t) cc_final: 0.8561 (p) REVERT: B 109 ASP cc_start: 0.7741 (m-30) cc_final: 0.7152 (OUTLIER) REVERT: B 114 TRP cc_start: 0.7865 (m-10) cc_final: 0.7584 (m-10) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.9792 time to fit residues: 41.7612 Evaluate side-chains 38 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 7 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.070442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.063884 restraints weight = 19211.668| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 4.45 r_work: 0.3761 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.8859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3240 Z= 0.182 Angle : 0.711 11.900 4401 Z= 0.341 Chirality : 0.044 0.166 477 Planarity : 0.005 0.049 567 Dihedral : 4.554 16.970 448 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.63 % Allowed : 21.93 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.52 (0.43), residues: 398 helix: -4.34 (0.48), residues: 25 sheet: 0.14 (0.46), residues: 136 loop : -0.08 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 114 HIS 0.001 0.000 HIS A 505 PHE 0.016 0.001 PHE B 65 TYR 0.011 0.001 TYR A 495 ARG 0.007 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 VAL cc_start: 0.8868 (t) cc_final: 0.8404 (p) REVERT: B 46 LEU cc_start: 0.8627 (mm) cc_final: 0.8224 (tp) REVERT: B 109 ASP cc_start: 0.7979 (m-30) cc_final: 0.7180 (t70) REVERT: B 114 TRP cc_start: 0.8069 (m-10) cc_final: 0.7772 (m-10) outliers start: 9 outliers final: 8 residues processed: 40 average time/residue: 0.8884 time to fit residues: 37.0658 Evaluate side-chains 39 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 0.0570 chunk 38 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.2100 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.068488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.061730 restraints weight = 18649.371| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 4.42 r_work: 0.3730 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.9120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3240 Z= 0.234 Angle : 0.744 11.636 4401 Z= 0.359 Chirality : 0.045 0.144 477 Planarity : 0.005 0.052 567 Dihedral : 4.813 17.506 448 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.34 % Allowed : 22.22 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.66 (0.43), residues: 398 helix: -4.60 (0.48), residues: 19 sheet: 0.12 (0.45), residues: 136 loop : -0.34 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 114 HIS 0.001 0.001 HIS A 505 PHE 0.017 0.002 PHE C 63 TYR 0.011 0.001 TYR C 92 ARG 0.006 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 VAL cc_start: 0.8937 (t) cc_final: 0.8437 (p) REVERT: B 46 LEU cc_start: 0.8740 (mm) cc_final: 0.8269 (tp) REVERT: B 109 ASP cc_start: 0.8146 (m-30) cc_final: 0.7153 (t70) REVERT: C 43 GLN cc_start: 0.8533 (tp40) cc_final: 0.8294 (tt0) outliers start: 8 outliers final: 7 residues processed: 40 average time/residue: 0.8725 time to fit residues: 36.5259 Evaluate side-chains 38 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 22 optimal weight: 0.0030 chunk 8 optimal weight: 20.0000 chunk 16 optimal weight: 0.0170 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.0870 chunk 19 optimal weight: 0.0670 chunk 0 optimal weight: 3.9990 overall best weight: 0.1544 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.070491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.063814 restraints weight = 18479.609| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 4.41 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.9076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3240 Z= 0.180 Angle : 0.743 11.204 4401 Z= 0.354 Chirality : 0.045 0.168 477 Planarity : 0.005 0.048 567 Dihedral : 4.323 15.717 448 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.58 % Allowed : 23.68 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.42 (0.43), residues: 398 helix: -4.49 (0.46), residues: 19 sheet: 0.30 (0.45), residues: 136 loop : -0.19 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.000 0.000 HIS A 505 PHE 0.015 0.001 PHE B 65 TYR 0.010 0.001 TYR A 495 ARG 0.006 0.001 ARG B 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 VAL cc_start: 0.8760 (t) cc_final: 0.8466 (p) REVERT: B 109 ASP cc_start: 0.7567 (m-30) cc_final: 0.6856 (t70) outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.9856 time to fit residues: 36.9832 Evaluate side-chains 35 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 0.0570 chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.069163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.062367 restraints weight = 18359.886| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 4.46 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.9272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3240 Z= 0.215 Angle : 0.739 10.908 4401 Z= 0.357 Chirality : 0.044 0.162 477 Planarity : 0.005 0.053 567 Dihedral : 4.487 15.782 448 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.17 % Allowed : 24.56 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.39 (0.43), residues: 398 helix: -4.59 (0.46), residues: 19 sheet: 0.35 (0.46), residues: 136 loop : -0.18 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 114 HIS 0.001 0.001 HIS A 505 PHE 0.019 0.002 PHE C 63 TYR 0.009 0.001 TYR A 495 ARG 0.004 0.000 ARG B 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2530.63 seconds wall clock time: 44 minutes 9.18 seconds (2649.18 seconds total)