Starting phenix.real_space_refine on Fri Aug 22 13:17:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xh8_33191/08_2025/7xh8_33191.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xh8_33191/08_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_33191/08_2025/7xh8_33191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xh8_33191/08_2025/7xh8_33191.map" model { file = "/net/cci-nas-00/data/ceres_data/7xh8_33191/08_2025/7xh8_33191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xh8_33191/08_2025/7xh8_33191.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.74, per 1000 atoms: 0.23 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: 0.15 Conformation dependent library (CDL) restraints added in 72.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.10 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: 0.28 Time building geometry restraints manager: 0.22 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.680 Find NCS groups from input model: 0.010 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:5.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.120 ------------------------------------------------------------------------------- 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= 0.846 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.018 0.003 ARG A 403 TYR 0.148 0.027 TYR A 489 PHE 0.087 0.017 PHE B 111 TRP 0.134 0.031 TRP C 97 HIS 0.009 0.006 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.01441 ( 3240) covalent geometry : angle 1.80730 ( 4401) hydrogen bonds : bond 0.14911 ( 114) hydrogen bonds : angle 8.49695 ( 267) *********************** 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 : 0.107 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: 0.6946 (m-80) outliers start: 3 outliers final: 0 residues processed: 120 average time/residue: 0.4843 time to fit residues: 59.4344 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 : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.079281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.072879 restraints weight = 18097.021| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 4.63 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3240 Z= 0.161 Angle : 0.786 11.015 4401 Z= 0.394 Chirality : 0.047 0.162 477 Planarity : 0.005 0.047 567 Dihedral : 5.935 45.222 448 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.92 % Allowed : 19.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.39), residues: 398 helix: -3.86 (0.59), residues: 27 sheet: -0.71 (0.40), residues: 146 loop : -0.31 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 88 TYR 0.016 0.001 TYR A 495 PHE 0.011 0.002 PHE C 99 TRP 0.016 0.002 TRP C 36 HIS 0.000 0.000 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3240) covalent geometry : angle 0.78644 ( 4401) hydrogen bonds : bond 0.03720 ( 114) hydrogen bonds : angle 6.73625 ( 267) *********************** 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 73 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 LYS cc_start: 0.9236 (tppt) cc_final: 0.8653 (tppt) REVERT: B 109 ASP cc_start: 0.7350 (m-30) cc_final: 0.6940 (t70) outliers start: 10 outliers final: 3 residues processed: 70 average time/residue: 0.4610 time to fit residues: 33.1552 Evaluate side-chains 48 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 74 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 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 = 0.4167 r_free = 0.4167 target = 0.077506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.070927 restraints weight = 18088.986| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 4.60 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3240 Z= 0.130 Angle : 0.719 12.500 4401 Z= 0.350 Chirality : 0.046 0.166 477 Planarity : 0.005 0.052 567 Dihedral : 5.225 37.991 448 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.41), residues: 398 helix: -3.71 (0.56), residues: 25 sheet: -0.55 (0.41), residues: 140 loop : -0.02 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 46 TYR 0.019 0.001 TYR B 81 PHE 0.008 0.001 PHE C 99 TRP 0.017 0.003 TRP B 37 HIS 0.003 0.002 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3240) covalent geometry : angle 0.71937 ( 4401) hydrogen bonds : bond 0.03461 ( 114) hydrogen bonds : angle 6.44848 ( 267) *********************** 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 60 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7954 (pm20) cc_final: 0.7605 (pp20) REVERT: B 35 MET cc_start: 0.7871 (tmm) cc_final: 0.7640 (tmm) REVERT: B 36 GLN cc_start: 0.6904 (pm20) cc_final: 0.6251 (pm20) outliers start: 9 outliers final: 4 residues processed: 58 average time/residue: 0.3618 time to fit residues: 21.7474 Evaluate side-chains 40 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain C residue 14 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.075090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.068451 restraints weight = 17977.195| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 4.57 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3240 Z= 0.157 Angle : 0.743 12.641 4401 Z= 0.359 Chirality : 0.046 0.161 477 Planarity : 0.005 0.044 567 Dihedral : 5.167 31.593 448 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.68 % Allowed : 18.42 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.41), residues: 398 helix: -4.10 (0.58), residues: 19 sheet: -0.31 (0.43), residues: 137 loop : -0.29 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 346 TYR 0.015 0.001 TYR A 495 PHE 0.009 0.001 PHE C 50 TRP 0.013 0.002 TRP B 114 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3240) covalent geometry : angle 0.74251 ( 4401) hydrogen bonds : bond 0.03353 ( 114) hydrogen bonds : angle 6.59926 ( 267) *********************** 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 57 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: B 81 TYR cc_start: 0.8312 (m-80) cc_final: 0.7969 (m-10) REVERT: B 109 ASP cc_start: 0.7472 (m-30) cc_final: 0.7132 (OUTLIER) REVERT: B 114 TRP cc_start: 0.8091 (m-10) cc_final: 0.7825 (m-10) REVERT: C 78 ARG cc_start: 0.6854 (tpp80) cc_final: 0.6000 (tpp80) outliers start: 16 outliers final: 6 residues processed: 53 average time/residue: 0.4054 time to fit residues: 22.2020 Evaluate side-chains 39 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ASP 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 74 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 30.0000 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.074148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.067485 restraints weight = 18361.685| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 4.64 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.7251 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= 0.138 Angle : 0.737 12.340 4401 Z= 0.357 Chirality : 0.045 0.178 477 Planarity : 0.004 0.043 567 Dihedral : 4.912 26.811 448 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.05 % Allowed : 19.59 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.41), residues: 398 helix: -3.97 (0.56), residues: 25 sheet: -0.32 (0.43), residues: 138 loop : -0.18 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 55 TYR 0.013 0.001 TYR A 495 PHE 0.007 0.001 PHE C 50 TRP 0.018 0.002 TRP C 36 HIS 0.001 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3240) covalent geometry : angle 0.73694 ( 4401) hydrogen bonds : bond 0.03187 ( 114) hydrogen bonds : angle 6.65801 ( 267) *********************** 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 48 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: B 38 VAL cc_start: 0.8870 (t) cc_final: 0.8546 (p) REVERT: B 109 ASP cc_start: 0.7773 (m-30) cc_final: 0.7189 (OUTLIER) REVERT: B 114 TRP cc_start: 0.7982 (m-10) cc_final: 0.7609 (m-10) REVERT: C 78 ARG cc_start: 0.6747 (tpp80) cc_final: 0.6225 (tpp80) REVERT: C 83 ASP cc_start: 0.6617 (m-30) cc_final: 0.6362 (m-30) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.3799 time to fit residues: 18.2044 Evaluate side-chains 40 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain B residue 5 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 0.0770 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.3940 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.070976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.064364 restraints weight = 18859.943| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 4.56 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.7815 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= 0.177 Angle : 0.759 14.120 4401 Z= 0.368 Chirality : 0.047 0.158 477 Planarity : 0.005 0.045 567 Dihedral : 5.092 21.767 448 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.22 % Allowed : 20.18 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.42), residues: 398 helix: -3.84 (0.59), residues: 25 sheet: -0.31 (0.44), residues: 138 loop : -0.25 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 403 TYR 0.013 0.001 TYR A 495 PHE 0.010 0.001 PHE C 37 TRP 0.017 0.002 TRP B 114 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 3240) covalent geometry : angle 0.75869 ( 4401) hydrogen bonds : bond 0.03317 ( 114) hydrogen bonds : angle 7.01444 ( 267) *********************** 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 46 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: B 38 VAL cc_start: 0.8859 (t) cc_final: 0.8559 (p) REVERT: B 109 ASP cc_start: 0.7598 (m-30) cc_final: 0.7133 (OUTLIER) outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 0.3624 time to fit residues: 16.1606 Evaluate side-chains 36 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 0.0270 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.072688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.066106 restraints weight = 19318.282| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 4.70 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.8073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3240 Z= 0.124 Angle : 0.736 11.990 4401 Z= 0.356 Chirality : 0.046 0.181 477 Planarity : 0.004 0.044 567 Dihedral : 4.713 20.652 448 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.63 % Allowed : 20.18 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.42), residues: 398 helix: -3.76 (0.53), residues: 33 sheet: -0.17 (0.45), residues: 135 loop : -0.20 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 46 TYR 0.013 0.001 TYR A 495 PHE 0.010 0.001 PHE C 37 TRP 0.010 0.001 TRP C 36 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3240) covalent geometry : angle 0.73558 ( 4401) hydrogen bonds : bond 0.03155 ( 114) hydrogen bonds : angle 6.65768 ( 267) *********************** 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 44 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: B 38 VAL cc_start: 0.8829 (t) cc_final: 0.8087 (p) REVERT: B 46 LEU cc_start: 0.8628 (mm) cc_final: 0.8210 (tp) REVERT: B 109 ASP cc_start: 0.7734 (m-30) cc_final: 0.7101 (OUTLIER) REVERT: C 64 SER cc_start: 0.7046 (p) cc_final: 0.6837 (t) outliers start: 9 outliers final: 5 residues processed: 41 average time/residue: 0.3086 time to fit residues: 13.2277 Evaluate side-chains 36 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 432 CYS 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 36 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.071035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.064601 restraints weight = 19659.698| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 4.59 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.8404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3240 Z= 0.154 Angle : 0.770 12.054 4401 Z= 0.373 Chirality : 0.046 0.177 477 Planarity : 0.005 0.045 567 Dihedral : 4.784 17.538 448 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.75 % Allowed : 22.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.42), residues: 398 helix: -4.10 (0.44), residues: 33 sheet: -0.03 (0.46), residues: 133 loop : -0.14 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 46 TYR 0.011 0.001 TYR A 495 PHE 0.006 0.001 PHE C 50 TRP 0.021 0.002 TRP C 36 HIS 0.002 0.002 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 3240) covalent geometry : angle 0.77032 ( 4401) hydrogen bonds : bond 0.03390 ( 114) hydrogen bonds : angle 6.84178 ( 267) *********************** 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 39 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: B 38 VAL cc_start: 0.8842 (t) cc_final: 0.8076 (p) REVERT: B 46 LEU cc_start: 0.8559 (mm) cc_final: 0.8173 (tp) REVERT: B 109 ASP cc_start: 0.7629 (m-30) cc_final: 0.7045 (OUTLIER) outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 0.2714 time to fit residues: 10.6439 Evaluate side-chains 35 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.6226 > 50: distance: 11 - 16: 22.265 distance: 16 - 17: 14.214 distance: 17 - 18: 12.558 distance: 17 - 20: 43.540 distance: 18 - 19: 40.108 distance: 18 - 25: 21.153 distance: 20 - 21: 45.668 distance: 21 - 22: 13.415 distance: 22 - 23: 25.835 distance: 22 - 24: 12.641 distance: 25 - 26: 6.447 distance: 26 - 27: 22.544 distance: 26 - 29: 33.986 distance: 27 - 28: 31.624 distance: 27 - 32: 14.909 distance: 29 - 30: 56.623 distance: 29 - 31: 41.865 distance: 32 - 33: 21.743 distance: 33 - 34: 32.214 distance: 33 - 36: 17.796 distance: 34 - 35: 16.985 distance: 34 - 41: 7.337 distance: 36 - 37: 40.317 distance: 37 - 38: 26.051 distance: 38 - 39: 15.368 distance: 39 - 40: 33.911 distance: 41 - 42: 11.859 distance: 42 - 43: 24.669 distance: 42 - 45: 21.023 distance: 43 - 44: 42.276 distance: 43 - 50: 12.285 distance: 45 - 46: 35.827 distance: 46 - 47: 13.696 distance: 47 - 48: 23.023 distance: 48 - 49: 36.753 distance: 50 - 51: 22.123 distance: 50 - 56: 15.652 distance: 51 - 52: 39.679 distance: 51 - 54: 31.541 distance: 52 - 53: 33.751 distance: 52 - 57: 35.823 distance: 54 - 55: 37.230 distance: 55 - 56: 22.488 distance: 57 - 58: 32.473 distance: 58 - 59: 19.641 distance: 59 - 60: 27.691 distance: 59 - 61: 48.575 distance: 61 - 62: 30.409 distance: 62 - 63: 9.977 distance: 62 - 65: 16.990 distance: 63 - 64: 5.482 distance: 63 - 68: 12.779 distance: 65 - 66: 52.654 distance: 65 - 67: 7.759 distance: 68 - 69: 25.823 distance: 69 - 70: 14.808 distance: 69 - 72: 40.690 distance: 70 - 71: 16.927 distance: 70 - 74: 9.570 distance: 72 - 73: 16.129 distance: 74 - 75: 14.454 distance: 74 - 121: 22.120 distance: 75 - 76: 44.549 distance: 75 - 78: 19.265 distance: 76 - 77: 23.747 distance: 76 - 81: 36.625 distance: 77 - 118: 24.206 distance: 78 - 79: 11.178 distance: 81 - 82: 20.507 distance: 82 - 83: 33.732 distance: 82 - 85: 9.317 distance: 83 - 84: 15.732 distance: 83 - 90: 23.836 distance: 85 - 86: 32.684 distance: 86 - 87: 37.841 distance: 87 - 88: 12.691 distance: 88 - 89: 9.742