Starting phenix.real_space_refine on Thu Mar 6 01:33:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dkw_27492/03_2025/8dkw_27492.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dkw_27492/03_2025/8dkw_27492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dkw_27492/03_2025/8dkw_27492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dkw_27492/03_2025/8dkw_27492.map" model { file = "/net/cci-nas-00/data/ceres_data/8dkw_27492/03_2025/8dkw_27492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dkw_27492/03_2025/8dkw_27492.cif" } resolution = 3.09 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= 0.004 sd= 0.082 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 15 5.16 5 C 2863 2.51 5 N 704 2.21 5 O 788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4370 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "B" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2680 Classifications: {'peptide': 334} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 15, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 3.73, per 1000 atoms: 0.85 Number of scatterers: 4370 At special positions: 0 Unit cell: (78.85, 63.91, 122.01, 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 15 16.00 O 788 8.00 N 704 7.00 C 2863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " 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: 1.18 Conformation dependent library (CDL) restraints added in 546.1 milliseconds 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 38.0% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.940A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.658A pdb=" N ASP A 91 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR A 92 " --> pdb=" O SER A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 92' Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.313A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 139 removed outlier: 3.902A pdb=" N SER P 124 " --> pdb=" O SER P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 152 removed outlier: 3.891A pdb=" N GLN P 145 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 182 removed outlier: 3.629A pdb=" N THR P 168 " --> pdb=" O ALA P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 194 Processing helix chain 'P' and resid 202 through 226 removed outlier: 3.500A pdb=" N TYR P 226 " --> pdb=" O GLN P 222 " (cutoff:3.500A) Processing helix chain 'P' and resid 234 through 258 Processing helix chain 'P' and resid 263 through 290 removed outlier: 3.531A pdb=" N VAL P 276 " --> pdb=" O ILE P 272 " (cutoff:3.500A) Proline residue: P 283 - end of helix Processing helix chain 'P' and resid 298 through 323 removed outlier: 4.093A pdb=" N LEU P 303 " --> pdb=" O ILE P 299 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU P 313 " --> pdb=" O GLY P 309 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN P 323 " --> pdb=" O GLN P 319 " (cutoff:3.500A) Processing helix chain 'P' and resid 334 through 356 removed outlier: 3.567A pdb=" N LEU P 338 " --> pdb=" O THR P 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.604A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 6 removed outlier: 12.172A pdb=" N CYS B 23 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 11.336A pdb=" N ALA B 74 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 11.467A pdb=" N ALA B 25 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N THR B 72 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N GLN B 27 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASP B 70 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.436A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 44 through 48 removed outlier: 6.356A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 26 through 27 Processing sheet with id=AA7, first strand: chain 'P' and resid 31 through 35 removed outlier: 6.934A pdb=" N VAL P 32 " --> pdb=" O LEU P 116 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE P 118 " --> pdb=" O VAL P 32 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU P 34 " --> pdb=" O ILE P 118 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR P 98 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 39 through 43 removed outlier: 3.596A pdb=" N THR P 90 " --> pdb=" O GLU P 71 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 597 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: 1.27 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1336 1.34 - 1.46: 932 1.46 - 1.57: 2200 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4490 Sorted by residual: bond pdb=" N ILE P 260 " pdb=" CA ILE P 260 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.00e+00 bond pdb=" N VAL P 259 " pdb=" CA VAL P 259 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.41e-02 5.03e+03 7.52e+00 bond pdb=" N TRP P 262 " pdb=" CA TRP P 262 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.37e-02 5.33e+03 6.84e+00 bond pdb=" N THR P 261 " pdb=" CA THR P 261 " ideal model delta sigma weight residual 1.460 1.500 -0.040 1.83e-02 2.99e+03 4.73e+00 bond pdb=" N GLY P 258 " pdb=" CA GLY P 258 " ideal model delta sigma weight residual 1.449 1.480 -0.031 1.45e-02 4.76e+03 4.53e+00 ... (remaining 4485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 5868 1.54 - 3.08: 203 3.08 - 4.63: 39 4.63 - 6.17: 10 6.17 - 7.71: 2 Bond angle restraints: 6122 Sorted by residual: angle pdb=" CA ILE P 260 " pdb=" C ILE P 260 " pdb=" O ILE P 260 " ideal model delta sigma weight residual 120.95 116.30 4.65 1.04e+00 9.25e-01 2.00e+01 angle pdb=" C THR P 261 " pdb=" CA THR P 261 " pdb=" CB THR P 261 " ideal model delta sigma weight residual 110.04 115.18 -5.14 1.51e+00 4.39e-01 1.16e+01 angle pdb=" C PRO P 195 " pdb=" N ASN P 196 " pdb=" CA ASN P 196 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.73e+00 angle pdb=" C ILE P 133 " pdb=" N TYR P 134 " pdb=" CA TYR P 134 " ideal model delta sigma weight residual 121.14 115.90 5.24 1.75e+00 3.27e-01 8.96e+00 angle pdb=" C ILE P 260 " pdb=" CA ILE P 260 " pdb=" CB ILE P 260 " ideal model delta sigma weight residual 112.14 115.64 -3.50 1.35e+00 5.49e-01 6.74e+00 ... (remaining 6117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 2316 17.84 - 35.68: 230 35.68 - 53.52: 32 53.52 - 71.36: 2 71.36 - 89.20: 3 Dihedral angle restraints: 2583 sinusoidal: 986 harmonic: 1597 Sorted by residual: dihedral pdb=" C THR P 261 " pdb=" N THR P 261 " pdb=" CA THR P 261 " pdb=" CB THR P 261 " ideal model delta harmonic sigma weight residual -122.00 -142.14 20.14 0 2.50e+00 1.60e-01 6.49e+01 dihedral pdb=" N THR P 261 " pdb=" C THR P 261 " pdb=" CA THR P 261 " pdb=" CB THR P 261 " ideal model delta harmonic sigma weight residual 123.40 142.24 -18.84 0 2.50e+00 1.60e-01 5.68e+01 dihedral pdb=" CA ARG P 112 " pdb=" C ARG P 112 " pdb=" N ILE P 113 " pdb=" CA ILE P 113 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 2580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 688 0.161 - 0.321: 4 0.321 - 0.482: 0 0.482 - 0.642: 0 0.642 - 0.803: 1 Chirality restraints: 693 Sorted by residual: chirality pdb=" CA THR P 261 " pdb=" N THR P 261 " pdb=" C THR P 261 " pdb=" CB THR P 261 " both_signs ideal model delta sigma weight residual False 2.53 1.72 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CB THR P 261 " pdb=" CA THR P 261 " pdb=" OG1 THR P 261 " pdb=" CG2 THR P 261 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB VAL P 259 " pdb=" CA VAL P 259 " pdb=" CG1 VAL P 259 " pdb=" CG2 VAL P 259 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 690 not shown) Planarity restraints: 764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP P 235 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO P 236 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO P 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO P 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG P 47 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO P 48 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO P 48 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO P 48 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 269 " 0.007 2.00e-02 2.50e+03 9.62e-03 1.62e+00 pdb=" CG PHE P 269 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE P 269 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE P 269 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE P 269 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE P 269 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE P 269 " -0.001 2.00e-02 2.50e+03 ... (remaining 761 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 77 2.66 - 3.22: 4170 3.22 - 3.78: 6492 3.78 - 4.34: 9068 4.34 - 4.90: 15515 Nonbonded interactions: 35322 Sorted by model distance: nonbonded pdb=" OH TYR P 134 " pdb=" OD1 ASP P 205 " model vdw 2.097 3.040 nonbonded pdb=" OE1 GLN B 6 " pdb=" OG1 THR B 102 " model vdw 2.169 3.040 nonbonded pdb=" NH2 ARG A 68 " pdb=" OD2 ASP A 91 " model vdw 2.181 3.120 nonbonded pdb=" OG1 THR A 40 " pdb=" O GLU A 42 " model vdw 2.183 3.040 nonbonded pdb=" OG1 THR A 28 " pdb=" OD1 ASN A 31 " model vdw 2.234 3.040 ... (remaining 35317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.990 Find NCS groups from input model: 0.040 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 0.045 4490 Z= 0.380 Angle : 0.711 7.709 6122 Z= 0.405 Chirality : 0.058 0.803 693 Planarity : 0.004 0.043 764 Dihedral : 13.839 89.198 1557 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.41 % Allowed : 7.47 % Favored : 92.12 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.31), residues: 547 helix: -0.87 (0.31), residues: 199 sheet: -2.01 (0.38), residues: 149 loop : -2.84 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 132 HIS 0.007 0.001 HIS B 55 PHE 0.022 0.001 PHE P 269 TYR 0.013 0.001 TYR A 100 ARG 0.006 0.001 ARG P 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.447 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8201 (tttp) cc_final: 0.7871 (tttm) REVERT: B 79 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8218 (mt0) REVERT: P 140 ILE cc_start: 0.7610 (tt) cc_final: 0.7170 (tp) REVERT: P 223 CYS cc_start: 0.7044 (p) cc_final: 0.6765 (p) outliers start: 2 outliers final: 0 residues processed: 63 average time/residue: 0.1675 time to fit residues: 13.5235 Evaluate side-chains 56 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.0040 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN B 6 GLN B 28 ASN B 38 GLN P 222 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.171761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132091 restraints weight = 4837.425| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.34 r_work: 0.3405 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4490 Z= 0.207 Angle : 0.579 6.692 6122 Z= 0.303 Chirality : 0.045 0.173 693 Planarity : 0.004 0.037 764 Dihedral : 4.925 18.916 596 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.87 % Allowed : 13.07 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.34), residues: 547 helix: 0.83 (0.35), residues: 197 sheet: -1.55 (0.41), residues: 136 loop : -2.42 (0.36), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 262 HIS 0.002 0.001 HIS B 55 PHE 0.017 0.001 PHE P 269 TYR 0.014 0.001 TYR P 134 ARG 0.005 0.001 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.460 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8172 (tttp) cc_final: 0.7745 (tttm) REVERT: B 79 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8067 (mt0) REVERT: P 140 ILE cc_start: 0.7717 (tt) cc_final: 0.7085 (tp) REVERT: P 148 MET cc_start: 0.7697 (tmm) cc_final: 0.7469 (tmm) REVERT: P 223 CYS cc_start: 0.7046 (p) cc_final: 0.6538 (p) REVERT: P 269 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.7011 (m-80) REVERT: P 332 ASP cc_start: 0.8464 (t0) cc_final: 0.8237 (t0) outliers start: 9 outliers final: 4 residues processed: 63 average time/residue: 0.1683 time to fit residues: 13.6812 Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN B 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.169356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130722 restraints weight = 4823.284| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.24 r_work: 0.3382 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4490 Z= 0.282 Angle : 0.587 7.143 6122 Z= 0.304 Chirality : 0.046 0.159 693 Planarity : 0.004 0.034 764 Dihedral : 4.961 18.654 596 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.49 % Allowed : 15.35 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.35), residues: 547 helix: 1.25 (0.36), residues: 197 sheet: -1.46 (0.40), residues: 149 loop : -2.30 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 235 HIS 0.003 0.001 HIS B 55 PHE 0.015 0.001 PHE P 269 TYR 0.016 0.001 TYR P 134 ARG 0.004 0.001 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.456 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8160 (tttp) cc_final: 0.7733 (tttm) REVERT: P 140 ILE cc_start: 0.7747 (tt) cc_final: 0.7116 (tp) REVERT: P 148 MET cc_start: 0.7770 (tmm) cc_final: 0.7417 (tmm) REVERT: P 269 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.7032 (m-80) outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 0.1517 time to fit residues: 12.9681 Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 330 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.168675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128533 restraints weight = 4928.773| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.37 r_work: 0.3411 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4490 Z= 0.222 Angle : 0.550 6.289 6122 Z= 0.285 Chirality : 0.045 0.151 693 Planarity : 0.003 0.032 764 Dihedral : 4.788 17.494 596 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.70 % Allowed : 17.01 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.79 (0.35), residues: 547 helix: 1.57 (0.36), residues: 197 sheet: -1.24 (0.44), residues: 136 loop : -2.05 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 235 HIS 0.002 0.000 HIS B 55 PHE 0.016 0.001 PHE P 269 TYR 0.014 0.001 TYR P 134 ARG 0.005 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.448 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8131 (tttp) cc_final: 0.7780 (tttm) REVERT: A 68 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7635 (ptm-80) REVERT: A 85 SER cc_start: 0.8394 (p) cc_final: 0.8069 (m) REVERT: B 61 ARG cc_start: 0.7727 (mtp180) cc_final: 0.7020 (ptm160) REVERT: B 82 ASP cc_start: 0.8376 (m-30) cc_final: 0.7662 (m-30) REVERT: P 148 MET cc_start: 0.7738 (tmm) cc_final: 0.7356 (tmm) REVERT: P 269 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.7036 (m-80) outliers start: 13 outliers final: 7 residues processed: 64 average time/residue: 0.1690 time to fit residues: 13.8731 Evaluate side-chains 63 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 0.3980 chunk 38 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.171210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133055 restraints weight = 4985.146| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.23 r_work: 0.3416 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4490 Z= 0.234 Angle : 0.548 6.244 6122 Z= 0.283 Chirality : 0.045 0.147 693 Planarity : 0.003 0.031 764 Dihedral : 4.753 17.056 596 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.32 % Allowed : 17.01 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.36), residues: 547 helix: 1.45 (0.36), residues: 203 sheet: -1.17 (0.45), residues: 136 loop : -1.90 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 132 HIS 0.001 0.000 HIS B 55 PHE 0.016 0.001 PHE P 269 TYR 0.015 0.001 TYR P 134 ARG 0.005 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.475 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8150 (tttp) cc_final: 0.7778 (tttm) REVERT: A 31 ASN cc_start: 0.8442 (m-40) cc_final: 0.8192 (m110) REVERT: A 55 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7411 (pm20) REVERT: A 85 SER cc_start: 0.8460 (p) cc_final: 0.8135 (m) REVERT: B 27 GLN cc_start: 0.8776 (tt0) cc_final: 0.8565 (mt0) REVERT: B 61 ARG cc_start: 0.7741 (mtp180) cc_final: 0.7147 (ptm160) REVERT: B 82 ASP cc_start: 0.8292 (m-30) cc_final: 0.7729 (m-30) REVERT: P 148 MET cc_start: 0.7735 (tmm) cc_final: 0.7345 (tmm) REVERT: P 180 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7844 (mp) REVERT: P 189 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: P 269 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7025 (m-80) outliers start: 16 outliers final: 7 residues processed: 69 average time/residue: 0.1608 time to fit residues: 14.3558 Evaluate side-chains 67 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 189 GLN Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 0.0370 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.173345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135539 restraints weight = 4855.174| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.21 r_work: 0.3428 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4490 Z= 0.194 Angle : 0.525 5.956 6122 Z= 0.272 Chirality : 0.044 0.144 693 Planarity : 0.003 0.030 764 Dihedral : 4.624 16.771 596 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.70 % Allowed : 18.67 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.55 (0.36), residues: 547 helix: 1.55 (0.36), residues: 205 sheet: -1.16 (0.44), residues: 142 loop : -1.74 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 132 HIS 0.001 0.000 HIS B 55 PHE 0.016 0.001 PHE P 269 TYR 0.013 0.001 TYR P 134 ARG 0.004 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.497 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8134 (tttp) cc_final: 0.7762 (tttm) REVERT: A 55 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: A 85 SER cc_start: 0.8438 (p) cc_final: 0.8076 (m) REVERT: B 61 ARG cc_start: 0.7743 (mtp180) cc_final: 0.7184 (ptm160) REVERT: B 82 ASP cc_start: 0.8169 (m-30) cc_final: 0.7557 (m-30) REVERT: P 67 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7134 (tp) REVERT: P 71 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8174 (mt-10) REVERT: P 148 MET cc_start: 0.7815 (tmm) cc_final: 0.7415 (tmm) REVERT: P 180 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7845 (mp) REVERT: P 189 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: P 269 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.7038 (m-80) outliers start: 13 outliers final: 8 residues processed: 66 average time/residue: 0.1619 time to fit residues: 13.9075 Evaluate side-chains 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 189 GLN Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 71.3107 > 50: distance: 14 - 193: 33.809 distance: 38 - 197: 34.732 distance: 41 - 194: 34.925 distance: 56 - 179: 37.586 distance: 59 - 176: 34.288 distance: 73 - 159: 35.640 distance: 76 - 156: 34.221 distance: 123 - 127: 33.966 distance: 127 - 128: 60.190 distance: 128 - 129: 21.126 distance: 128 - 131: 17.752 distance: 129 - 130: 40.818 distance: 132 - 133: 40.266 distance: 133 - 135: 18.241 distance: 136 - 137: 46.473 distance: 137 - 138: 9.751 distance: 137 - 140: 42.309 distance: 138 - 144: 69.162 distance: 140 - 141: 40.983 distance: 141 - 142: 4.393 distance: 145 - 146: 39.876 distance: 146 - 147: 40.588 distance: 148 - 149: 56.959 distance: 156 - 157: 69.299 distance: 157 - 160: 39.058 distance: 164 - 165: 56.855 distance: 165 - 168: 13.676 distance: 166 - 167: 46.347 distance: 168 - 169: 47.704 distance: 169 - 170: 55.653 distance: 170 - 172: 39.373 distance: 172 - 174: 58.167 distance: 173 - 174: 26.190 distance: 174 - 175: 13.749 distance: 176 - 177: 40.799 distance: 177 - 178: 35.774 distance: 177 - 180: 40.376 distance: 181 - 182: 37.491 distance: 182 - 184: 19.115 distance: 183 - 185: 39.231 distance: 184 - 186: 39.597 distance: 185 - 186: 22.696 distance: 186 - 187: 18.550 distance: 188 - 189: 39.954 distance: 189 - 192: 39.156 distance: 194 - 195: 56.466 distance: 195 - 196: 40.963 distance: 195 - 198: 9.329 distance: 196 - 197: 6.163 distance: 196 - 199: 40.107 distance: 200 - 201: 56.942 distance: 200 - 203: 41.195 distance: 201 - 210: 33.925 distance: 203 - 204: 56.544 distance: 204 - 205: 48.401 distance: 205 - 206: 4.009 distance: 206 - 207: 24.844