Starting phenix.real_space_refine on Fri Aug 2 19:33:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/08_2024/8efp_28087.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/08_2024/8efp_28087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/08_2024/8efp_28087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/08_2024/8efp_28087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/08_2024/8efp_28087.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/08_2024/8efp_28087.cif" } resolution = 3.8 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= 0.000 sd= 0.009 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 13 5.16 5 C 2977 2.51 5 N 808 2.21 5 O 907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 59": "OE1" <-> "OE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 160": "OE1" <-> "OE2" Residue "C PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C GLU 351": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4705 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1976 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} Chain: "C" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2729 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Time building chain proxies: 3.18, per 1000 atoms: 0.68 Number of scatterers: 4705 At special positions: 0 Unit cell: (76.176, 74.52, 113.436, 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 13 16.00 O 907 8.00 N 808 7.00 C 2977 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: 1.88 Conformation dependent library (CDL) restraints added in 847.9 milliseconds 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 40.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.524A pdb=" N PHE B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 Processing helix chain 'C' and resid 4 through 18 removed outlier: 3.527A pdb=" N ALA C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 68 through 77 removed outlier: 4.179A pdb=" N ASP C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 143 through 150 removed outlier: 3.660A pdb=" N ARG C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 removed outlier: 4.258A pdb=" N HIS C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 Processing helix chain 'C' and resid 264 through 279 Processing helix chain 'C' and resid 281 through 299 Processing helix chain 'C' and resid 307 through 315 Processing helix chain 'C' and resid 322 through 339 Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 354 through 369 Processing helix chain 'C' and resid 371 through 376 Processing helix chain 'C' and resid 383 through 404 Processing sheet with id=AA1, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.594A pdb=" N LEU B 82 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 102 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 161 through 163 removed outlier: 3.521A pdb=" N CYS B 183 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS B 204 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN B 230 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TYR B 206 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 22 through 24 removed outlier: 3.853A pdb=" N SER C 206 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU C 160 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS C 210 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL C 158 " --> pdb=" O LYS C 210 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 522 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: 1.11 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 959 1.33 - 1.45: 1038 1.45 - 1.57: 2773 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4790 Sorted by residual: bond pdb=" N LEU C 263 " pdb=" CA LEU C 263 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.14e-02 7.69e+03 1.42e+01 bond pdb=" N ASP C 173 " pdb=" CA ASP C 173 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.70e-03 1.06e+04 9.06e+00 bond pdb=" N LYS C 177 " pdb=" CA LYS C 177 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.26e-02 6.30e+03 8.83e+00 bond pdb=" CA LYS C 177 " pdb=" C LYS C 177 " ideal model delta sigma weight residual 1.519 1.534 -0.016 5.30e-03 3.56e+04 8.82e+00 bond pdb=" N THR C 264 " pdb=" CA THR C 264 " ideal model delta sigma weight residual 1.454 1.494 -0.039 1.33e-02 5.65e+03 8.68e+00 ... (remaining 4785 not shown) Histogram of bond angle deviations from ideal: 89.70 - 98.69: 12 98.69 - 107.69: 227 107.69 - 116.68: 3118 116.68 - 125.68: 3075 125.68 - 134.67: 63 Bond angle restraints: 6495 Sorted by residual: angle pdb=" C PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta sigma weight residual 113.37 93.25 20.12 1.61e+00 3.86e-01 1.56e+02 angle pdb=" N SER C 180 " pdb=" CA SER C 180 " pdb=" C SER C 180 " ideal model delta sigma weight residual 112.94 95.36 17.58 1.41e+00 5.03e-01 1.56e+02 angle pdb=" N PRO C 215 " pdb=" CA PRO C 215 " pdb=" C PRO C 215 " ideal model delta sigma weight residual 111.19 94.15 17.04 1.57e+00 4.06e-01 1.18e+02 angle pdb=" N GLN C 194 " pdb=" CA GLN C 194 " pdb=" C GLN C 194 " ideal model delta sigma weight residual 108.23 89.70 18.53 1.72e+00 3.38e-01 1.16e+02 angle pdb=" N ARG C 195 " pdb=" CA ARG C 195 " pdb=" C ARG C 195 " ideal model delta sigma weight residual 108.76 93.60 15.16 1.69e+00 3.50e-01 8.05e+01 ... (remaining 6490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 2474 18.18 - 36.37: 360 36.37 - 54.55: 101 54.55 - 72.73: 11 72.73 - 90.91: 8 Dihedral angle restraints: 2954 sinusoidal: 1197 harmonic: 1757 Sorted by residual: dihedral pdb=" C PHE B 98 " pdb=" N PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta harmonic sigma weight residual -122.60 -97.68 -24.92 0 2.50e+00 1.60e-01 9.94e+01 dihedral pdb=" C VAL C 213 " pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" CB VAL C 213 " ideal model delta harmonic sigma weight residual -122.00 -103.01 -18.99 0 2.50e+00 1.60e-01 5.77e+01 dihedral pdb=" C GLN C 194 " pdb=" N GLN C 194 " pdb=" CA GLN C 194 " pdb=" CB GLN C 194 " ideal model delta harmonic sigma weight residual -122.60 -104.35 -18.25 0 2.50e+00 1.60e-01 5.33e+01 ... (remaining 2951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 709 0.147 - 0.293: 30 0.293 - 0.440: 3 0.440 - 0.586: 0 0.586 - 0.733: 5 Chirality restraints: 747 Sorted by residual: chirality pdb=" CA VAL C 213 " pdb=" N VAL C 213 " pdb=" C VAL C 213 " pdb=" CB VAL C 213 " both_signs ideal model delta sigma weight residual False 2.44 3.17 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA TYR C 176 " pdb=" N TYR C 176 " pdb=" C TYR C 176 " pdb=" CB TYR C 176 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CA TRP C 179 " pdb=" N TRP C 179 " pdb=" C TRP C 179 " pdb=" CB TRP C 179 " both_signs ideal model delta sigma weight residual False 2.51 3.13 -0.62 2.00e-01 2.50e+01 9.68e+00 ... (remaining 744 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 95 " -0.024 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C LEU B 95 " 0.080 2.00e-02 2.50e+03 pdb=" O LEU B 95 " -0.029 2.00e-02 2.50e+03 pdb=" N PRO B 96 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 37 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C ASN B 37 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN B 37 " -0.018 2.00e-02 2.50e+03 pdb=" N SER B 38 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 398 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ILE C 398 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE C 398 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU C 399 " -0.013 2.00e-02 2.50e+03 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 64 2.51 - 3.10: 3894 3.10 - 3.70: 7797 3.70 - 4.30: 10845 4.30 - 4.90: 16554 Nonbonded interactions: 39154 Sorted by model distance: nonbonded pdb=" O TRP C 179 " pdb=" CG TRP C 179 " model vdw 1.908 3.260 nonbonded pdb=" O TRP C 179 " pdb=" CD2 TRP C 179 " model vdw 2.113 3.260 nonbonded pdb=" N VAL C 213 " pdb=" O VAL C 213 " model vdw 2.191 2.496 nonbonded pdb=" OG1 THR C 151 " pdb=" NH1 ARG C 152 " model vdw 2.219 3.120 nonbonded pdb=" O LYS C 359 " pdb=" N VAL C 362 " model vdw 2.258 3.120 ... (remaining 39149 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.010 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 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 0.052 4790 Z= 0.385 Angle : 1.460 20.115 6495 Z= 0.886 Chirality : 0.085 0.733 747 Planarity : 0.007 0.067 848 Dihedral : 18.607 90.911 1804 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 33.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer: Outliers : 3.07 % Allowed : 31.03 % Favored : 65.90 % Cbeta Deviations : 1.22 % 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: -4.26 (0.29), residues: 586 helix: -2.31 (0.31), residues: 203 sheet: -3.30 (0.61), residues: 49 loop : -3.21 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 34 HIS 0.006 0.001 HIS B 26 PHE 0.021 0.003 PHE B 98 TYR 0.027 0.002 TYR C 129 ARG 0.008 0.001 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 TYR cc_start: 0.7911 (m-10) cc_final: 0.7477 (m-10) REVERT: C 275 LEU cc_start: 0.8243 (pp) cc_final: 0.7875 (pp) outliers start: 16 outliers final: 4 residues processed: 77 average time/residue: 0.1822 time to fit residues: 17.8058 Evaluate side-chains 50 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain C residue 86 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 0.0270 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 HIS B 87 ASN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN C 186 HIS ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4790 Z= 0.263 Angle : 0.888 11.610 6495 Z= 0.446 Chirality : 0.047 0.162 747 Planarity : 0.006 0.067 848 Dihedral : 7.617 59.333 647 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 3.26 % Allowed : 29.69 % Favored : 67.05 % 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: -3.89 (0.30), residues: 586 helix: -1.86 (0.31), residues: 212 sheet: -3.48 (0.56), residues: 54 loop : -3.01 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP C 179 HIS 0.005 0.001 HIS C 51 PHE 0.017 0.002 PHE C 34 TYR 0.018 0.001 TYR B 27 ARG 0.011 0.001 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.8913 (pp) cc_final: 0.8335 (mt) REVERT: B 108 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.5467 (pmt-80) REVERT: C 275 LEU cc_start: 0.8240 (pp) cc_final: 0.7940 (pp) outliers start: 17 outliers final: 10 residues processed: 67 average time/residue: 0.1810 time to fit residues: 15.6819 Evaluate side-chains 56 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 394 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 4790 Z= 0.333 Angle : 0.856 11.622 6495 Z= 0.431 Chirality : 0.044 0.138 747 Planarity : 0.006 0.073 848 Dihedral : 7.134 52.889 645 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 27.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.46 % Favored : 87.54 % Rotamer: Outliers : 4.41 % Allowed : 28.54 % Favored : 67.05 % 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: -3.77 (0.31), residues: 586 helix: -1.61 (0.30), residues: 223 sheet: -3.49 (0.49), residues: 74 loop : -2.96 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 34 HIS 0.007 0.002 HIS C 186 PHE 0.014 0.002 PHE B 192 TYR 0.013 0.002 TYR B 27 ARG 0.005 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 47 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.6381 (OUTLIER) cc_final: 0.5293 (pmt-80) REVERT: C 15 GLU cc_start: 0.8608 (tp30) cc_final: 0.8329 (mm-30) REVERT: C 62 LEU cc_start: 0.9401 (tt) cc_final: 0.9173 (mm) outliers start: 23 outliers final: 11 residues processed: 66 average time/residue: 0.1804 time to fit residues: 15.3257 Evaluate side-chains 51 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 394 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN C 286 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 4790 Z= 0.367 Angle : 0.871 11.723 6495 Z= 0.434 Chirality : 0.045 0.166 747 Planarity : 0.006 0.067 848 Dihedral : 6.956 32.210 643 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 29.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.65 % Favored : 86.35 % Rotamer: Outliers : 4.21 % Allowed : 27.59 % Favored : 68.20 % 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: -3.44 (0.32), residues: 586 helix: -1.20 (0.32), residues: 211 sheet: -3.43 (0.51), residues: 68 loop : -2.86 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 69 HIS 0.005 0.002 HIS C 186 PHE 0.018 0.002 PHE B 48 TYR 0.016 0.002 TYR C 156 ARG 0.005 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 44 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.9723 (tp) cc_final: 0.9437 (pt) REVERT: B 108 ARG cc_start: 0.6260 (OUTLIER) cc_final: 0.5414 (pmt-80) REVERT: B 145 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: C 62 LEU cc_start: 0.9373 (tt) cc_final: 0.9114 (mm) REVERT: C 275 LEU cc_start: 0.8028 (pp) cc_final: 0.7755 (pp) outliers start: 22 outliers final: 12 residues processed: 63 average time/residue: 0.1649 time to fit residues: 13.5912 Evaluate side-chains 54 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 379 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 39 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 4790 Z= 0.297 Angle : 0.819 11.092 6495 Z= 0.407 Chirality : 0.045 0.172 747 Planarity : 0.005 0.062 848 Dihedral : 6.698 33.024 643 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 26.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 3.45 % Allowed : 29.12 % Favored : 67.43 % 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: -3.31 (0.32), residues: 586 helix: -1.05 (0.32), residues: 223 sheet: -3.99 (0.46), residues: 55 loop : -2.79 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 34 HIS 0.005 0.001 HIS C 186 PHE 0.011 0.002 PHE C 315 TYR 0.012 0.002 TYR B 227 ARG 0.004 0.001 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 44 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.9726 (tp) cc_final: 0.9448 (pt) REVERT: B 108 ARG cc_start: 0.6339 (OUTLIER) cc_final: 0.5299 (pmt-80) REVERT: C 62 LEU cc_start: 0.9347 (tt) cc_final: 0.9081 (mm) REVERT: C 275 LEU cc_start: 0.7977 (pp) cc_final: 0.7717 (pp) outliers start: 18 outliers final: 12 residues processed: 56 average time/residue: 0.1650 time to fit residues: 12.2831 Evaluate side-chains 52 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 392 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** C 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4790 Z= 0.234 Angle : 0.794 13.152 6495 Z= 0.387 Chirality : 0.043 0.132 747 Planarity : 0.005 0.057 848 Dihedral : 6.320 31.636 643 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 3.26 % Allowed : 29.12 % Favored : 67.62 % 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: -2.80 (0.33), residues: 586 helix: -0.58 (0.33), residues: 217 sheet: -3.54 (0.50), residues: 67 loop : -2.46 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 179 HIS 0.004 0.001 HIS C 186 PHE 0.012 0.002 PHE C 315 TYR 0.010 0.001 TYR B 227 ARG 0.003 0.000 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.9699 (tp) cc_final: 0.9421 (pt) REVERT: B 75 LEU cc_start: 0.9054 (pp) cc_final: 0.8700 (mt) REVERT: B 108 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5207 (pmt-80) REVERT: B 230 ASN cc_start: 0.8541 (t0) cc_final: 0.8329 (t0) REVERT: C 62 LEU cc_start: 0.9368 (tt) cc_final: 0.9129 (mm) REVERT: C 281 LYS cc_start: 0.9361 (mmtt) cc_final: 0.9139 (mmtt) REVERT: C 308 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8766 (mmmm) outliers start: 17 outliers final: 10 residues processed: 61 average time/residue: 0.1824 time to fit residues: 14.2433 Evaluate side-chains 56 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 379 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 0.0060 chunk 31 optimal weight: 8.9990 chunk 56 optimal weight: 0.1980 chunk 35 optimal weight: 0.0020 chunk 34 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 17 optimal weight: 0.0670 chunk 11 optimal weight: 0.7980 overall best weight: 0.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN B 257 GLN ** C 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4790 Z= 0.199 Angle : 0.794 12.978 6495 Z= 0.384 Chirality : 0.043 0.139 747 Planarity : 0.004 0.052 848 Dihedral : 6.057 30.509 643 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 2.11 % Allowed : 29.12 % Favored : 68.77 % 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: -2.69 (0.34), residues: 586 helix: -0.54 (0.33), residues: 217 sheet: -3.74 (0.47), residues: 78 loop : -2.17 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 34 HIS 0.006 0.001 HIS B 209 PHE 0.013 0.001 PHE C 315 TYR 0.011 0.001 TYR C 176 ARG 0.006 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.9656 (tp) cc_final: 0.9385 (pt) REVERT: B 75 LEU cc_start: 0.9016 (pp) cc_final: 0.8689 (mt) REVERT: B 108 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.4914 (pmt-80) REVERT: B 194 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: B 258 ILE cc_start: 0.9281 (pt) cc_final: 0.8823 (mt) REVERT: C 62 LEU cc_start: 0.9400 (tt) cc_final: 0.9173 (mm) REVERT: C 85 GLN cc_start: 0.7478 (mm110) cc_final: 0.7243 (tp-100) REVERT: C 308 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8798 (mmmm) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 0.1800 time to fit residues: 13.2638 Evaluate side-chains 51 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 308 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN ** C 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4790 Z= 0.259 Angle : 0.799 10.480 6495 Z= 0.388 Chirality : 0.042 0.135 747 Planarity : 0.005 0.055 848 Dihedral : 6.110 30.607 643 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 2.30 % Allowed : 29.50 % Favored : 68.20 % 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: -2.55 (0.34), residues: 586 helix: -0.47 (0.33), residues: 213 sheet: -3.67 (0.48), residues: 78 loop : -2.03 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 34 HIS 0.004 0.001 HIS C 186 PHE 0.010 0.002 PHE B 220 TYR 0.014 0.001 TYR C 382 ARG 0.005 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.9681 (tp) cc_final: 0.9416 (pt) REVERT: B 75 LEU cc_start: 0.9086 (pp) cc_final: 0.8693 (mt) REVERT: B 108 ARG cc_start: 0.6351 (OUTLIER) cc_final: 0.5232 (pmt-80) REVERT: B 258 ILE cc_start: 0.9380 (pt) cc_final: 0.8962 (mt) REVERT: C 62 LEU cc_start: 0.9385 (tt) cc_final: 0.9153 (mm) REVERT: C 85 GLN cc_start: 0.7539 (mm110) cc_final: 0.7274 (tp-100) REVERT: C 308 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8816 (mmmm) outliers start: 12 outliers final: 5 residues processed: 55 average time/residue: 0.2108 time to fit residues: 14.8065 Evaluate side-chains 52 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 308 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-dev-5409/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-dev-5409/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: 52.7468 > 50: distance: 41 - 51: 3.094 distance: 66 - 90: 15.716 distance: 70 - 95: 9.069 distance: 78 - 103: 11.635 distance: 84 - 90: 14.115 distance: 85 - 111: 8.326 distance: 90 - 91: 9.509 distance: 91 - 92: 22.671 distance: 91 - 94: 13.177 distance: 92 - 93: 24.826 distance: 92 - 95: 14.313 distance: 93 - 120: 12.085 distance: 95 - 96: 11.568 distance: 96 - 97: 14.404 distance: 96 - 99: 13.842 distance: 97 - 98: 8.422 distance: 97 - 103: 6.037 distance: 99 - 100: 13.827 distance: 100 - 101: 19.070 distance: 100 - 102: 14.611 distance: 103 - 104: 12.277 distance: 104 - 105: 8.804 distance: 104 - 107: 15.651 distance: 105 - 106: 11.366 distance: 105 - 111: 13.313 distance: 107 - 108: 17.803 distance: 108 - 109: 18.425 distance: 108 - 110: 12.479 distance: 111 - 112: 10.749 distance: 112 - 113: 3.075 distance: 112 - 115: 3.435 distance: 113 - 114: 13.600 distance: 113 - 120: 11.838 distance: 115 - 116: 22.966 distance: 116 - 117: 15.197 distance: 117 - 118: 14.528 distance: 117 - 119: 26.283 distance: 120 - 121: 11.031 distance: 121 - 122: 8.812 distance: 121 - 124: 13.800 distance: 122 - 123: 18.013 distance: 122 - 128: 16.740 distance: 124 - 125: 17.489 distance: 125 - 126: 8.513 distance: 125 - 127: 14.514 distance: 128 - 129: 4.785 distance: 129 - 130: 11.233 distance: 129 - 132: 7.208 distance: 130 - 131: 7.929 distance: 130 - 134: 8.194 distance: 132 - 133: 11.945 distance: 134 - 135: 7.765 distance: 135 - 136: 17.670 distance: 135 - 138: 5.620 distance: 136 - 137: 5.877 distance: 136 - 143: 19.372 distance: 138 - 139: 9.955 distance: 139 - 140: 6.214 distance: 140 - 141: 15.000 distance: 140 - 142: 18.977 distance: 143 - 144: 16.632 distance: 144 - 145: 34.239 distance: 144 - 147: 16.186 distance: 145 - 146: 13.036 distance: 145 - 152: 40.934 distance: 146 - 180: 22.751 distance: 147 - 148: 17.390 distance: 148 - 149: 11.109 distance: 149 - 150: 29.302 distance: 149 - 151: 20.085 distance: 152 - 153: 17.469 distance: 153 - 154: 15.878 distance: 153 - 156: 21.280 distance: 154 - 155: 14.764 distance: 154 - 161: 17.731 distance: 155 - 187: 13.997 distance: 156 - 157: 4.580 distance: 157 - 158: 10.721 distance: 158 - 159: 8.185 distance: 158 - 160: 4.853 distance: 161 - 162: 9.075 distance: 162 - 163: 10.292 distance: 162 - 165: 6.721 distance: 163 - 164: 8.303 distance: 163 - 170: 7.201 distance: 164 - 191: 18.018 distance: 165 - 166: 19.143 distance: 167 - 169: 10.890