Starting phenix.real_space_refine on Sat Apr 26 16:00:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x64_38079/04_2025/8x64_38079.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x64_38079/04_2025/8x64_38079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x64_38079/04_2025/8x64_38079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x64_38079/04_2025/8x64_38079.map" model { file = "/net/cci-nas-00/data/ceres_data/8x64_38079/04_2025/8x64_38079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x64_38079/04_2025/8x64_38079.cif" } resolution = 3.4 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= 0.056 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 C 1472 2.51 5 N 351 2.21 5 O 345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2189 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2167 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 3 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y5R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.45, per 1000 atoms: 1.12 Number of scatterers: 2189 At special positions: 0 Unit cell: (54.06, 73.14, 71.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 20 16.00 O 345 8.00 N 351 7.00 C 1472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 444 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 244.3 milliseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 510 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 81.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'B' and resid 27 through 53 removed outlier: 3.669A pdb=" N CYS B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 40 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 removed outlier: 3.909A pdb=" N ILE B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 69 " --> pdb=" O TYR B 65 " (cutoff:3.500A) Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 96 through 130 removed outlier: 3.825A pdb=" N CYS B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 165 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 187 through 220 removed outlier: 3.509A pdb=" N LYS B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 409 through 439 Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 447 through 472 removed outlier: 3.644A pdb=" N MET B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 452 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) Proline residue: B 465 - end of helix Proline residue: B 469 - end of helix Processing helix chain 'B' and resid 475 through 480 151 hydrogen bonds defined for protein. 453 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: 0.53 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 305 1.30 - 1.43: 644 1.43 - 1.56: 1268 1.56 - 1.68: 2 1.68 - 1.81: 32 Bond restraints: 2251 Sorted by residual: bond pdb=" C PHE B 424 " pdb=" N ILE B 425 " ideal model delta sigma weight residual 1.332 1.257 0.075 1.36e-02 5.41e+03 3.04e+01 bond pdb=" C PHE B 424 " pdb=" O PHE B 424 " ideal model delta sigma weight residual 1.235 1.172 0.064 1.26e-02 6.30e+03 2.55e+01 bond pdb=" CA PHE B 424 " pdb=" CB PHE B 424 " ideal model delta sigma weight residual 1.530 1.447 0.084 1.69e-02 3.50e+03 2.44e+01 bond pdb=" CA PHE B 424 " pdb=" C PHE B 424 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.34e-02 5.57e+03 2.32e+01 bond pdb=" N PHE B 424 " pdb=" CA PHE B 424 " ideal model delta sigma weight residual 1.457 1.396 0.061 1.29e-02 6.01e+03 2.27e+01 ... (remaining 2246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 2924 1.66 - 3.31: 94 3.31 - 4.97: 25 4.97 - 6.62: 8 6.62 - 8.28: 3 Bond angle restraints: 3054 Sorted by residual: angle pdb=" CA ALA B 423 " pdb=" C ALA B 423 " pdb=" N PHE B 424 " ideal model delta sigma weight residual 117.30 124.60 -7.30 1.16e+00 7.43e-01 3.96e+01 angle pdb=" O ALA B 423 " pdb=" C ALA B 423 " pdb=" N PHE B 424 " ideal model delta sigma weight residual 122.12 116.20 5.92 1.06e+00 8.90e-01 3.12e+01 angle pdb=" N PHE B 424 " pdb=" CA PHE B 424 " pdb=" C PHE B 424 " ideal model delta sigma weight residual 110.80 102.52 8.28 2.13e+00 2.20e-01 1.51e+01 angle pdb=" CA ILE B 115 " pdb=" C ILE B 115 " pdb=" N PHE B 116 " ideal model delta sigma weight residual 116.60 121.79 -5.19 1.45e+00 4.76e-01 1.28e+01 angle pdb=" N ALA B 423 " pdb=" CA ALA B 423 " pdb=" C ALA B 423 " ideal model delta sigma weight residual 111.28 114.76 -3.48 1.09e+00 8.42e-01 1.02e+01 ... (remaining 3049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.25: 1116 14.25 - 28.50: 145 28.50 - 42.74: 52 42.74 - 56.99: 7 56.99 - 71.24: 1 Dihedral angle restraints: 1321 sinusoidal: 538 harmonic: 783 Sorted by residual: dihedral pdb=" CB CYS B 441 " pdb=" SG CYS B 441 " pdb=" SG CYS B 444 " pdb=" CB CYS B 444 " ideal model delta sinusoidal sigma weight residual -86.00 -142.50 56.50 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" C ILE B 115 " pdb=" N ILE B 115 " pdb=" CA ILE B 115 " pdb=" CB ILE B 115 " ideal model delta harmonic sigma weight residual -122.00 -134.73 12.73 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CA ILE B 115 " pdb=" CB ILE B 115 " ideal model delta harmonic sigma weight residual 123.40 135.77 -12.37 0 2.50e+00 1.60e-01 2.45e+01 ... (remaining 1318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 328 0.085 - 0.169: 20 0.169 - 0.254: 0 0.254 - 0.339: 0 0.339 - 0.423: 1 Chirality restraints: 349 Sorted by residual: chirality pdb=" CA ILE B 115 " pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CB ILE B 115 " both_signs ideal model delta sigma weight residual False 2.43 2.01 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA MET B 81 " pdb=" N MET B 81 " pdb=" C MET B 81 " pdb=" CB MET B 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CB ILE B 115 " pdb=" CA ILE B 115 " pdb=" CG1 ILE B 115 " pdb=" CG2 ILE B 115 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 346 not shown) Planarity restraints: 358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 424 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C PHE B 424 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE B 424 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE B 425 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C SER B 114 " 0.052 2.00e-02 2.50e+03 pdb=" O SER B 114 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE B 115 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 78 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C ALA B 78 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA B 78 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL B 79 " -0.015 2.00e-02 2.50e+03 ... (remaining 355 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 609 2.81 - 3.33: 2228 3.33 - 3.86: 3460 3.86 - 4.38: 3778 4.38 - 4.90: 6258 Nonbonded interactions: 16333 Sorted by model distance: nonbonded pdb=" OG1 THR B 41 " pdb=" OG1 THR B 462 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASP B 73 " pdb=" OG SER B 461 " model vdw 2.296 3.040 nonbonded pdb=" O PHE B 424 " pdb=" C ILE B 425 " model vdw 2.317 3.270 nonbonded pdb=" O ALA B 423 " pdb=" ND2 ASN B 460 " model vdw 2.380 3.120 nonbonded pdb=" OH TYR B 214 " pdb=" NZ LYS B 218 " model vdw 2.384 3.120 ... (remaining 16328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 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: 0.680 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.630 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:2.960 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 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 : 0.006 0.084 2253 Z= 0.358 Angle : 0.789 8.277 3058 Z= 0.428 Chirality : 0.048 0.423 349 Planarity : 0.007 0.047 358 Dihedral : 14.113 71.238 805 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.42 % Allowed : 0.00 % Favored : 99.58 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.53), residues: 255 helix: 0.47 (0.37), residues: 194 sheet: None (None), residues: 0 loop : -3.69 (0.72), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 455 HIS 0.003 0.001 HIS B 450 PHE 0.010 0.001 PHE B 435 TYR 0.018 0.001 TYR B 200 ARG 0.004 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.11981 ( 151) hydrogen bonds : angle 6.27632 ( 453) SS BOND : bond 0.00082 ( 2) SS BOND : angle 0.64590 ( 4) covalent geometry : bond 0.00598 ( 2251) covalent geometry : angle 0.78918 ( 3054) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.276 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1379 time to fit residues: 7.0946 Evaluate side-chains 36 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.0010 chunk 23 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.252500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.222236 restraints weight = 2772.733| |-----------------------------------------------------------------------------| r_work (start): 0.4491 rms_B_bonded: 3.31 r_work: 0.4338 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2253 Z= 0.152 Angle : 0.659 7.450 3058 Z= 0.334 Chirality : 0.041 0.125 349 Planarity : 0.005 0.041 358 Dihedral : 5.577 50.887 299 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.67 % Allowed : 14.23 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.53), residues: 255 helix: 0.95 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -3.52 (0.73), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 455 HIS 0.001 0.001 HIS B 167 PHE 0.012 0.001 PHE B 435 TYR 0.010 0.001 TYR B 126 ARG 0.001 0.000 ARG B 411 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 151) hydrogen bonds : angle 4.73967 ( 453) SS BOND : bond 0.00170 ( 2) SS BOND : angle 0.57237 ( 4) covalent geometry : bond 0.00344 ( 2251) covalent geometry : angle 0.65896 ( 3054) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.246 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.1438 time to fit residues: 6.6302 Evaluate side-chains 34 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.0670 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.227665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.200226 restraints weight = 2955.068| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 3.20 r_work: 0.4227 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5722 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2253 Z= 0.172 Angle : 0.680 7.296 3058 Z= 0.347 Chirality : 0.042 0.139 349 Planarity : 0.005 0.042 358 Dihedral : 5.647 48.757 299 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.35 % Allowed : 17.15 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.53), residues: 255 helix: 0.99 (0.36), residues: 194 sheet: None (None), residues: 0 loop : -3.59 (0.73), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 455 HIS 0.002 0.001 HIS B 167 PHE 0.013 0.001 PHE B 435 TYR 0.012 0.002 TYR B 126 ARG 0.002 0.000 ARG B 411 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 151) hydrogen bonds : angle 4.84171 ( 453) SS BOND : bond 0.00175 ( 2) SS BOND : angle 0.64048 ( 4) covalent geometry : bond 0.00396 ( 2251) covalent geometry : angle 0.67986 ( 3054) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.246 Fit side-chains REVERT: B 206 MET cc_start: 0.4695 (ttm) cc_final: 0.4488 (ttm) outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 0.1396 time to fit residues: 6.9711 Evaluate side-chains 38 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 438 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.225685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.199346 restraints weight = 2813.912| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 3.05 r_work: 0.4226 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5741 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2253 Z= 0.174 Angle : 0.675 7.169 3058 Z= 0.344 Chirality : 0.043 0.143 349 Planarity : 0.005 0.040 358 Dihedral : 5.657 48.830 299 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.35 % Allowed : 20.50 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.53), residues: 255 helix: 0.99 (0.36), residues: 194 sheet: None (None), residues: 0 loop : -3.50 (0.73), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 455 HIS 0.001 0.001 HIS B 167 PHE 0.014 0.001 PHE B 435 TYR 0.011 0.002 TYR B 126 ARG 0.002 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 151) hydrogen bonds : angle 4.81980 ( 453) SS BOND : bond 0.00161 ( 2) SS BOND : angle 0.51738 ( 4) covalent geometry : bond 0.00401 ( 2251) covalent geometry : angle 0.67520 ( 3054) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.256 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 40 average time/residue: 0.1392 time to fit residues: 6.7307 Evaluate side-chains 43 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 438 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 19 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.235976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.209254 restraints weight = 2693.506| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 2.85 r_work: 0.4273 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5722 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2253 Z= 0.170 Angle : 0.679 7.087 3058 Z= 0.348 Chirality : 0.043 0.147 349 Planarity : 0.005 0.039 358 Dihedral : 5.673 49.058 299 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.60 % Allowed : 20.50 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.52), residues: 255 helix: 0.95 (0.36), residues: 196 sheet: None (None), residues: 0 loop : -3.29 (0.77), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 455 HIS 0.001 0.001 HIS B 167 PHE 0.017 0.001 PHE B 435 TYR 0.011 0.002 TYR B 126 ARG 0.002 0.000 ARG B 411 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 151) hydrogen bonds : angle 4.85347 ( 453) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.50064 ( 4) covalent geometry : bond 0.00391 ( 2251) covalent geometry : angle 0.67941 ( 3054) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.254 Fit side-chains REVERT: B 428 TRP cc_start: 0.7241 (OUTLIER) cc_final: 0.6813 (m-10) REVERT: B 454 ILE cc_start: 0.6955 (OUTLIER) cc_final: 0.6718 (mt) outliers start: 11 outliers final: 5 residues processed: 46 average time/residue: 0.1271 time to fit residues: 7.1813 Evaluate side-chains 45 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 428 TRP Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 454 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.229269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.203106 restraints weight = 2851.689| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 3.09 r_work: 0.4244 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2253 Z= 0.146 Angle : 0.666 11.096 3058 Z= 0.331 Chirality : 0.042 0.187 349 Planarity : 0.005 0.038 358 Dihedral : 5.515 48.934 299 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.18 % Allowed : 20.50 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.53), residues: 255 helix: 1.04 (0.36), residues: 196 sheet: None (None), residues: 0 loop : -3.35 (0.75), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 455 HIS 0.001 0.001 HIS B 59 PHE 0.013 0.001 PHE B 435 TYR 0.008 0.001 TYR B 126 ARG 0.001 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 151) hydrogen bonds : angle 4.75837 ( 453) SS BOND : bond 0.00141 ( 2) SS BOND : angle 0.40630 ( 4) covalent geometry : bond 0.00329 ( 2251) covalent geometry : angle 0.66673 ( 3054) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.261 Fit side-chains REVERT: B 428 TRP cc_start: 0.7191 (OUTLIER) cc_final: 0.6843 (m-10) REVERT: B 454 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6731 (mt) outliers start: 10 outliers final: 6 residues processed: 42 average time/residue: 0.1358 time to fit residues: 6.8741 Evaluate side-chains 43 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 428 TRP Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 454 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.233175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.206089 restraints weight = 2691.077| |-----------------------------------------------------------------------------| r_work (start): 0.4394 rms_B_bonded: 2.86 r_work: 0.4243 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2253 Z= 0.184 Angle : 0.722 11.263 3058 Z= 0.363 Chirality : 0.044 0.191 349 Planarity : 0.005 0.038 358 Dihedral : 5.715 50.090 299 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.02 % Allowed : 20.92 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.52), residues: 255 helix: 0.82 (0.36), residues: 196 sheet: None (None), residues: 0 loop : -3.40 (0.76), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 455 HIS 0.001 0.001 HIS B 167 PHE 0.018 0.001 PHE B 435 TYR 0.013 0.002 TYR B 126 ARG 0.002 0.000 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.04422 ( 151) hydrogen bonds : angle 4.94319 ( 453) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.49875 ( 4) covalent geometry : bond 0.00426 ( 2251) covalent geometry : angle 0.72238 ( 3054) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: B 428 TRP cc_start: 0.7389 (OUTLIER) cc_final: 0.6937 (m-10) REVERT: B 454 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6751 (mt) outliers start: 12 outliers final: 6 residues processed: 44 average time/residue: 0.1506 time to fit residues: 7.8343 Evaluate side-chains 44 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 428 TRP Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 454 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.315 > 50: distance: 31 - 36: 34.191 distance: 36 - 37: 48.177 distance: 37 - 38: 43.474 distance: 38 - 39: 24.288 distance: 38 - 40: 42.210 distance: 40 - 41: 14.617 distance: 41 - 42: 67.487 distance: 41 - 44: 38.926 distance: 42 - 43: 56.787 distance: 42 - 51: 31.064 distance: 43 - 72: 42.811 distance: 45 - 46: 39.756 distance: 46 - 47: 14.055 distance: 47 - 48: 20.708 distance: 48 - 49: 37.511 distance: 48 - 50: 45.392 distance: 51 - 52: 32.758 distance: 51 - 57: 40.757 distance: 52 - 53: 40.088 distance: 52 - 55: 4.142 distance: 53 - 54: 40.715 distance: 53 - 58: 38.101 distance: 54 - 80: 57.047 distance: 55 - 56: 4.933 distance: 58 - 59: 12.415 distance: 59 - 60: 15.489 distance: 59 - 62: 21.076 distance: 60 - 66: 41.133 distance: 61 - 91: 47.621 distance: 62 - 63: 30.754 distance: 63 - 64: 42.496 distance: 63 - 65: 28.277 distance: 66 - 67: 6.721 distance: 67 - 68: 32.172 distance: 68 - 69: 10.250 distance: 68 - 72: 14.894 distance: 69 - 105: 43.415 distance: 71 - 169: 35.154 distance: 72 - 73: 31.711 distance: 73 - 74: 16.196 distance: 73 - 76: 34.110 distance: 74 - 75: 40.948 distance: 74 - 80: 43.376 distance: 75 - 113: 38.214 distance: 76 - 77: 37.641 distance: 77 - 78: 25.621 distance: 80 - 81: 31.887 distance: 81 - 82: 42.940 distance: 81 - 84: 17.761 distance: 82 - 83: 6.841 distance: 82 - 91: 42.099 distance: 83 - 119: 27.201 distance: 84 - 85: 11.472 distance: 85 - 86: 29.001 distance: 85 - 87: 25.656 distance: 86 - 88: 11.848 distance: 87 - 89: 35.101 distance: 88 - 90: 31.441 distance: 89 - 90: 42.522 distance: 91 - 92: 13.443 distance: 92 - 93: 42.606 distance: 92 - 95: 40.801 distance: 93 - 94: 7.890 distance: 93 - 105: 25.644 distance: 94 - 126: 27.053 distance: 95 - 96: 25.132 distance: 96 - 97: 16.917 distance: 96 - 98: 13.203 distance: 97 - 99: 28.563 distance: 98 - 100: 5.231 distance: 98 - 101: 25.169 distance: 99 - 100: 41.209 distance: 100 - 102: 45.226 distance: 101 - 103: 25.957 distance: 102 - 104: 17.173 distance: 103 - 104: 21.167 distance: 105 - 106: 21.029 distance: 107 - 108: 69.318 distance: 108 - 132: 35.748 distance: 109 - 110: 39.850 distance: 110 - 111: 51.911 distance: 110 - 112: 40.262 distance: 113 - 114: 8.732 distance: 114 - 115: 40.778 distance: 114 - 117: 45.698 distance: 115 - 116: 56.764 distance: 115 - 119: 33.446 distance: 116 - 141: 36.267 distance: 117 - 118: 46.856