Starting phenix.real_space_refine on Thu Dec 7 16:15:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/12_2023/8jpf_36478_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/12_2023/8jpf_36478.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/12_2023/8jpf_36478_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/12_2023/8jpf_36478_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/12_2023/8jpf_36478_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/12_2023/8jpf_36478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/12_2023/8jpf_36478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/12_2023/8jpf_36478_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpf_36478/12_2023/8jpf_36478_updated.pdb" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.049 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 11 5.16 5 C 1481 2.51 5 N 383 2.21 5 O 393 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 166": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2269 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "R" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2178 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 3, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 123 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'SRW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.88, per 1000 atoms: 0.83 Number of scatterers: 2269 At special positions: 0 Unit cell: (48.616, 63.448, 83.224, 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) S 11 16.00 F 1 9.00 O 393 8.00 N 383 7.00 C 1481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.09 Conformation dependent library (CDL) restraints added in 400.4 milliseconds 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 1 sheets defined 77.6% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'R' and resid 60 through 87 removed outlier: 3.772A pdb=" N VAL R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 126 removed outlier: 3.722A pdb=" N MET R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 137 through 171 removed outlier: 3.505A pdb=" N ARG R 142 " --> pdb=" O ASP R 138 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR R 145 " --> pdb=" O CYS R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 179 Processing helix chain 'R' and resid 182 through 199 Processing helix chain 'R' and resid 201 through 206 Processing helix chain 'R' and resid 230 through 244 Processing helix chain 'R' and resid 246 through 270 Processing helix chain 'R' and resid 294 through 328 removed outlier: 3.991A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 336 through 367 removed outlier: 4.026A pdb=" N MET R 347 " --> pdb=" O HIS R 343 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER R 356 " --> pdb=" O LEU R 352 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN R 360 " --> pdb=" O SER R 356 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 369 through 377 Processing sheet with id= A, first strand: chain 'R' and resid 209 through 211 176 hydrogen bonds defined for protein. 519 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: 0.58 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 372 1.33 - 1.45: 641 1.45 - 1.57: 1295 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 2324 Sorted by residual: bond pdb=" C13 SRW R 501 " pdb=" N2 SRW R 501 " ideal model delta sigma weight residual 1.329 1.209 0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C15 SRW R 501 " pdb=" N3 SRW R 501 " ideal model delta sigma weight residual 1.348 1.457 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C13 SRW R 501 " pdb=" C16 SRW R 501 " ideal model delta sigma weight residual 1.387 1.290 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C14 SRW R 501 " pdb=" N3 SRW R 501 " ideal model delta sigma weight residual 1.362 1.453 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" CA ARG R 166 " pdb=" C ARG R 166 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.29e-02 6.01e+03 7.63e+00 ... (remaining 2319 not shown) Histogram of bond angle deviations from ideal: 56.78 - 72.61: 3 72.61 - 88.43: 0 88.43 - 104.26: 29 104.26 - 120.08: 2137 120.08 - 135.91: 1023 Bond angle restraints: 3192 Sorted by residual: angle pdb=" C24 SRW R 501 " pdb=" C14 SRW R 501 " pdb=" N3 SRW R 501 " ideal model delta sigma weight residual 71.53 118.99 -47.46 3.00e+00 1.11e-01 2.50e+02 angle pdb=" C24 SRW R 501 " pdb=" C14 SRW R 501 " pdb=" N2 SRW R 501 " ideal model delta sigma weight residual 162.48 118.92 43.56 3.00e+00 1.11e-01 2.11e+02 angle pdb=" C19 SRW R 501 " pdb=" C18 SRW R 501 " pdb=" N4 SRW R 501 " ideal model delta sigma weight residual 84.97 121.56 -36.59 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C17 SRW R 501 " pdb=" C18 SRW R 501 " pdb=" N4 SRW R 501 " ideal model delta sigma weight residual 154.40 120.08 34.32 3.00e+00 1.11e-01 1.31e+02 angle pdb=" N1 SRW R 501 " pdb=" C13 SRW R 501 " pdb=" N2 SRW R 501 " ideal model delta sigma weight residual 87.58 119.11 -31.53 3.00e+00 1.11e-01 1.10e+02 ... (remaining 3187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 1248 21.89 - 43.78: 76 43.78 - 65.68: 8 65.68 - 87.57: 2 87.57 - 109.46: 4 Dihedral angle restraints: 1338 sinusoidal: 440 harmonic: 898 Sorted by residual: dihedral pdb=" C8 SRW R 501 " pdb=" C11 SRW R 501 " pdb=" C12 SRW R 501 " pdb=" N1 SRW R 501 " ideal model delta sinusoidal sigma weight residual 52.96 -56.50 109.46 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C8 SRW R 501 " pdb=" C10 SRW R 501 " pdb=" C9 SRW R 501 " pdb=" N1 SRW R 501 " ideal model delta sinusoidal sigma weight residual -52.93 49.36 -102.29 1 3.00e+01 1.11e-03 1.29e+01 dihedral pdb=" CA HIS R 132 " pdb=" C HIS R 132 " pdb=" N PRO R 133 " pdb=" CA PRO R 133 " ideal model delta harmonic sigma weight residual 180.00 -162.28 -17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 1335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.075: 391 1.075 - 2.149: 0 2.149 - 3.224: 0 3.224 - 4.299: 0 4.299 - 5.374: 1 Chirality restraints: 392 Sorted by residual: chirality pdb=" C8 SRW R 501 " pdb=" C12 SRW R 501 " pdb=" C3 SRW R 501 " pdb=" C9 SRW R 501 " both_signs ideal model delta sigma weight residual False 2.71 -2.66 5.37 2.00e-01 2.50e+01 7.22e+02 chirality pdb=" CA VAL R 56 " pdb=" N VAL R 56 " pdb=" C VAL R 56 " pdb=" CB VAL R 56 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA VAL R 223 " pdb=" N VAL R 223 " pdb=" C VAL R 223 " pdb=" CB VAL R 223 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.34e-01 ... (remaining 389 not shown) Planarity restraints: 391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS R 132 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO R 133 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO R 133 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 133 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 165 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.11e+00 pdb=" C GLU R 165 " -0.018 2.00e-02 2.50e+03 pdb=" O GLU R 165 " 0.007 2.00e-02 2.50e+03 pdb=" N ARG R 166 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 166 " 0.004 2.00e-02 2.50e+03 8.62e-03 7.43e-01 pdb=" C ARG R 166 " -0.015 2.00e-02 2.50e+03 pdb=" O ARG R 166 " 0.006 2.00e-02 2.50e+03 pdb=" N TYR R 167 " 0.005 2.00e-02 2.50e+03 ... (remaining 388 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 331 2.75 - 3.29: 2438 3.29 - 3.83: 4003 3.83 - 4.36: 4232 4.36 - 4.90: 7704 Nonbonded interactions: 18708 Sorted by model distance: nonbonded pdb=" OE1 GLU R 123 " pdb=" OH TYR R 354 " model vdw 2.214 2.440 nonbonded pdb=" OD2 ASP R 112 " pdb=" ND2 ASN R 360 " model vdw 2.347 2.520 nonbonded pdb=" OH TYR L 11 " pdb=" O LEU R 54 " model vdw 2.352 2.440 nonbonded pdb=" O GLU R 123 " pdb=" N ILE R 128 " model vdw 2.410 2.520 nonbonded pdb=" OD1 ASP R 138 " pdb=" N ALA R 139 " model vdw 2.414 2.520 ... (remaining 18703 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 6.640 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.340 Find NCS groups from input model: 0.060 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 0.120 2324 Z= 0.414 Angle : 1.757 47.456 3192 Z= 0.646 Chirality : 0.274 5.374 392 Planarity : 0.004 0.037 391 Dihedral : 15.609 109.459 754 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.46 % Allowed : 7.34 % Favored : 92.20 % 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: 2.25 (0.48), residues: 296 helix: 2.15 (0.32), residues: 232 sheet: None (None), residues: 0 loop : -1.00 (0.78), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 134 HIS 0.003 0.001 HIS R 343 PHE 0.012 0.001 PHE R 375 TYR 0.014 0.002 TYR R 319 ARG 0.004 0.000 ARG R 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.277 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.2151 time to fit residues: 10.2037 Evaluate side-chains 36 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN R 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2324 Z= 0.193 Angle : 0.603 6.712 3192 Z= 0.300 Chirality : 0.040 0.146 392 Planarity : 0.004 0.033 391 Dihedral : 7.060 63.648 340 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.29 % Allowed : 7.80 % Favored : 89.91 % 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: 2.19 (0.48), residues: 296 helix: 2.16 (0.32), residues: 231 sheet: -3.87 (1.03), residues: 10 loop : -0.56 (0.85), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 134 HIS 0.004 0.001 HIS R 343 PHE 0.016 0.002 PHE R 375 TYR 0.016 0.002 TYR R 364 ARG 0.003 0.001 ARG R 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.233 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.1721 time to fit residues: 9.3155 Evaluate side-chains 45 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.248 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0344 time to fit residues: 0.5469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN R 238 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2324 Z= 0.206 Angle : 0.603 7.252 3192 Z= 0.299 Chirality : 0.040 0.127 392 Planarity : 0.004 0.036 391 Dihedral : 8.019 67.384 340 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.46 % Allowed : 11.47 % Favored : 88.07 % 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: 2.14 (0.48), residues: 296 helix: 2.12 (0.32), residues: 229 sheet: -3.49 (1.13), residues: 10 loop : -0.51 (0.84), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.015 0.002 PHE R 375 TYR 0.014 0.002 TYR R 364 ARG 0.002 0.000 ARG R 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.289 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.1880 time to fit residues: 9.3138 Evaluate side-chains 41 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2324 Z= 0.257 Angle : 0.623 6.945 3192 Z= 0.314 Chirality : 0.042 0.138 392 Planarity : 0.004 0.037 391 Dihedral : 8.708 69.653 340 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.75 % Allowed : 11.47 % Favored : 85.78 % 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: 1.83 (0.48), residues: 296 helix: 1.92 (0.32), residues: 229 sheet: -3.11 (1.33), residues: 10 loop : -0.81 (0.83), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.017 0.002 PHE R 353 TYR 0.024 0.002 TYR R 364 ARG 0.004 0.000 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.262 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 0.1828 time to fit residues: 9.2935 Evaluate side-chains 43 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.248 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0256 time to fit residues: 0.5106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.0060 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 0.0040 overall best weight: 0.9610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2324 Z= 0.222 Angle : 0.598 6.654 3192 Z= 0.303 Chirality : 0.041 0.132 392 Planarity : 0.004 0.038 391 Dihedral : 9.035 73.396 340 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.46 % Allowed : 11.93 % Favored : 87.61 % 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: 1.83 (0.48), residues: 296 helix: 1.94 (0.33), residues: 229 sheet: -2.91 (1.54), residues: 10 loop : -0.95 (0.80), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.015 0.002 PHE R 205 TYR 0.013 0.002 TYR R 319 ARG 0.005 0.001 ARG R 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.248 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.1646 time to fit residues: 8.3036 Evaluate side-chains 40 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.0000 chunk 21 optimal weight: 3.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2324 Z= 0.180 Angle : 0.557 6.766 3192 Z= 0.282 Chirality : 0.039 0.122 392 Planarity : 0.004 0.038 391 Dihedral : 9.225 82.061 340 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.38 % Allowed : 13.76 % Favored : 84.86 % 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: 1.97 (0.48), residues: 296 helix: 1.99 (0.32), residues: 229 sheet: -2.35 (1.77), residues: 10 loop : -0.77 (0.82), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 134 HIS 0.002 0.001 HIS R 320 PHE 0.014 0.001 PHE R 205 TYR 0.013 0.002 TYR R 364 ARG 0.004 0.001 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.249 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.1685 time to fit residues: 8.4753 Evaluate side-chains 42 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.247 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0271 time to fit residues: 0.3796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2324 Z= 0.194 Angle : 0.580 6.755 3192 Z= 0.293 Chirality : 0.041 0.172 392 Planarity : 0.004 0.038 391 Dihedral : 9.408 87.325 340 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.92 % Allowed : 16.06 % Favored : 83.03 % 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: 1.93 (0.48), residues: 296 helix: 1.98 (0.32), residues: 227 sheet: -2.01 (1.85), residues: 10 loop : -0.85 (0.80), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 134 HIS 0.003 0.001 HIS R 104 PHE 0.014 0.002 PHE R 205 TYR 0.029 0.003 TYR R 364 ARG 0.002 0.000 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.263 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 0.1718 time to fit residues: 8.4072 Evaluate side-chains 41 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.246 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2324 Z= 0.242 Angle : 0.615 7.080 3192 Z= 0.316 Chirality : 0.041 0.130 392 Planarity : 0.004 0.038 391 Dihedral : 10.012 98.546 340 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.83 % Allowed : 16.06 % Favored : 82.11 % 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: 1.76 (0.47), residues: 296 helix: 1.85 (0.32), residues: 228 sheet: -1.63 (1.91), residues: 10 loop : -1.04 (0.79), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.016 0.002 PHE R 205 TYR 0.026 0.003 TYR R 364 ARG 0.005 0.001 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.253 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.1741 time to fit residues: 8.0831 Evaluate side-chains 43 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.217 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0240 time to fit residues: 0.3900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2324 Z= 0.191 Angle : 0.622 12.687 3192 Z= 0.311 Chirality : 0.040 0.126 392 Planarity : 0.004 0.038 391 Dihedral : 9.920 99.217 340 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.38 % Allowed : 15.60 % Favored : 83.03 % 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: 1.84 (0.48), residues: 296 helix: 1.93 (0.32), residues: 227 sheet: -1.75 (1.91), residues: 10 loop : -1.01 (0.80), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 134 HIS 0.002 0.001 HIS R 320 PHE 0.015 0.001 PHE R 205 TYR 0.025 0.003 TYR R 70 ARG 0.003 0.000 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.265 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 42 average time/residue: 0.1684 time to fit residues: 8.2997 Evaluate side-chains 42 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.241 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0258 time to fit residues: 0.3689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2324 Z= 0.205 Angle : 0.621 11.988 3192 Z= 0.314 Chirality : 0.040 0.133 392 Planarity : 0.004 0.038 391 Dihedral : 10.061 101.655 340 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.92 % Allowed : 17.43 % Favored : 81.65 % 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: 1.77 (0.48), residues: 296 helix: 1.92 (0.32), residues: 228 sheet: -1.58 (1.94), residues: 10 loop : -1.31 (0.81), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 134 HIS 0.002 0.001 HIS R 320 PHE 0.015 0.002 PHE R 205 TYR 0.024 0.003 TYR R 364 ARG 0.006 0.001 ARG L 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.250 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 0.1755 time to fit residues: 8.9950 Evaluate side-chains 41 residues out of total 263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.0964 > 50: distance: 95 - 120: 4.893 distance: 107 - 128: 4.386 distance: 111 - 133: 13.624 distance: 115 - 120: 3.532 distance: 116 - 141: 9.707 distance: 120 - 121: 3.885 distance: 121 - 124: 6.570 distance: 123 - 152: 5.877 distance: 124 - 125: 4.262 distance: 125 - 126: 7.251 distance: 125 - 127: 21.669 distance: 128 - 129: 7.435 distance: 129 - 132: 10.123 distance: 130 - 131: 11.145 distance: 130 - 133: 9.471 distance: 131 - 164: 24.787 distance: 133 - 134: 17.017 distance: 134 - 135: 11.750 distance: 134 - 137: 15.176 distance: 135 - 136: 3.532 distance: 137 - 138: 17.012 distance: 138 - 139: 19.643 distance: 138 - 140: 24.277 distance: 141 - 142: 6.039 distance: 142 - 143: 11.866 distance: 142 - 145: 3.808 distance: 143 - 144: 12.523 distance: 143 - 152: 3.984 distance: 145 - 146: 6.572 distance: 146 - 147: 5.015 distance: 146 - 148: 20.052 distance: 147 - 149: 17.321 distance: 148 - 150: 31.057 distance: 149 - 151: 7.993 distance: 150 - 151: 14.357 distance: 152 - 153: 18.497 distance: 153 - 154: 15.419 distance: 153 - 156: 19.353 distance: 154 - 155: 23.601 distance: 154 - 164: 9.628 distance: 156 - 157: 13.511 distance: 157 - 158: 5.971 distance: 157 - 159: 17.082 distance: 158 - 160: 17.258 distance: 159 - 161: 20.561 distance: 160 - 162: 9.235 distance: 161 - 162: 18.489 distance: 162 - 163: 17.429 distance: 164 - 165: 6.848 distance: 165 - 166: 7.793 distance: 165 - 168: 3.418 distance: 166 - 167: 15.800 distance: 166 - 171: 9.361 distance: 167 - 190: 19.803 distance: 168 - 169: 17.204 distance: 168 - 170: 18.348 distance: 171 - 172: 12.912 distance: 172 - 173: 9.606 distance: 172 - 175: 4.893 distance: 173 - 174: 12.043 distance: 173 - 177: 6.399 distance: 175 - 176: 26.571 distance: 177 - 178: 4.343 distance: 178 - 179: 6.288 distance: 178 - 181: 7.230 distance: 179 - 180: 20.669 distance: 179 - 183: 22.906 distance: 181 - 182: 14.305 distance: 183 - 184: 25.401 distance: 184 - 185: 28.055 distance: 184 - 187: 14.960 distance: 185 - 186: 22.658 distance: 185 - 190: 21.148 distance: 187 - 188: 20.689 distance: 187 - 189: 19.831 distance: 190 - 191: 17.832 distance: 191 - 192: 14.391 distance: 191 - 194: 23.309 distance: 192 - 193: 19.065 distance: 192 - 198: 12.770 distance: 194 - 195: 24.183 distance: 194 - 196: 11.219 distance: 195 - 197: 17.883 distance: 201 - 222: 3.239