Starting phenix.real_space_refine on Thu Dec 7 20:52:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/12_2023/6nt5_0502_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/12_2023/6nt5_0502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/12_2023/6nt5_0502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/12_2023/6nt5_0502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/12_2023/6nt5_0502_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/12_2023/6nt5_0502_neut.pdb" } resolution = 4.1 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= 0.003 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 24 5.16 5 C 2952 2.51 5 N 798 2.21 5 O 812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4586 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2293 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2293 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 2.92, per 1000 atoms: 0.64 Number of scatterers: 4586 At special positions: 0 Unit cell: (78.12, 73.08, 104.16, 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 24 16.00 O 812 8.00 N 798 7.00 C 2952 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: 1.81 Conformation dependent library (CDL) restraints added in 873.2 milliseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1100 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 60.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 17 through 33 removed outlier: 3.846A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 70 removed outlier: 3.763A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 91 through 105 removed outlier: 3.612A pdb=" N ARG A 95 " --> pdb=" O CYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 134 removed outlier: 3.765A pdb=" N LEU A 123 " --> pdb=" O TRP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 156 through 167 removed outlier: 3.684A pdb=" N ALA A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 167 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 183 through 188 removed outlier: 4.134A pdb=" N ASN A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 4.179A pdb=" N THR A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.528A pdb=" N ALA A 277 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 278 " --> pdb=" O SER A 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 278' Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.746A pdb=" N ASP A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.699A pdb=" N GLU A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 33 removed outlier: 3.846A pdb=" N LEU B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 70 removed outlier: 3.762A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 91 through 105 removed outlier: 3.612A pdb=" N ARG B 95 " --> pdb=" O CYS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 134 removed outlier: 3.766A pdb=" N LEU B 123 " --> pdb=" O TRP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'B' and resid 156 through 167 removed outlier: 3.683A pdb=" N ALA B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 167 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 183 through 188 removed outlier: 4.134A pdb=" N ASN B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 273 removed outlier: 4.179A pdb=" N THR B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.529A pdb=" N ALA B 277 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 278 " --> pdb=" O SER B 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 278' Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.748A pdb=" N ASP B 301 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.699A pdb=" N GLU B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 223 removed outlier: 5.944A pdb=" N PHE A 221 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLU A 246 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A 255 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU A 198 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE A 312 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE A 200 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR A 314 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 202 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 219 through 223 removed outlier: 5.945A pdb=" N PHE B 221 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLU B 246 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY B 255 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU B 198 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 312 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ILE B 200 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR B 314 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 202 " --> pdb=" O TYR B 314 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 702 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: 1.19 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1437 1.34 - 1.45: 710 1.45 - 1.57: 2501 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 4676 Sorted by residual: bond pdb=" CA GLY B 90 " pdb=" C GLY B 90 " ideal model delta sigma weight residual 1.530 1.511 0.020 1.04e-02 9.25e+03 3.67e+00 bond pdb=" CA GLY A 90 " pdb=" C GLY A 90 " ideal model delta sigma weight residual 1.530 1.511 0.019 1.04e-02 9.25e+03 3.50e+00 bond pdb=" N GLY B 90 " pdb=" CA GLY B 90 " ideal model delta sigma weight residual 1.464 1.447 0.018 1.12e-02 7.97e+03 2.44e+00 bond pdb=" N GLY A 90 " pdb=" CA GLY A 90 " ideal model delta sigma weight residual 1.464 1.447 0.017 1.12e-02 7.97e+03 2.36e+00 bond pdb=" C PRO A 11 " pdb=" N CYS A 12 " ideal model delta sigma weight residual 1.329 1.300 0.029 1.86e-02 2.89e+03 2.35e+00 ... (remaining 4671 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.98: 138 106.98 - 113.72: 2647 113.72 - 120.47: 1984 120.47 - 127.21: 1519 127.21 - 133.96: 54 Bond angle restraints: 6342 Sorted by residual: angle pdb=" N LEU B 172 " pdb=" CA LEU B 172 " pdb=" C LEU B 172 " ideal model delta sigma weight residual 109.81 121.12 -11.31 2.21e+00 2.05e-01 2.62e+01 angle pdb=" N LEU A 172 " pdb=" CA LEU A 172 " pdb=" C LEU A 172 " ideal model delta sigma weight residual 109.81 121.11 -11.30 2.21e+00 2.05e-01 2.62e+01 angle pdb=" C GLY B 151 " pdb=" N ASN B 152 " pdb=" CA ASN B 152 " ideal model delta sigma weight residual 122.08 128.79 -6.71 1.47e+00 4.63e-01 2.09e+01 angle pdb=" C GLY A 151 " pdb=" N ASN A 152 " pdb=" CA ASN A 152 " ideal model delta sigma weight residual 122.08 128.75 -6.67 1.47e+00 4.63e-01 2.06e+01 angle pdb=" C PRO A 11 " pdb=" N CYS A 12 " pdb=" CA CYS A 12 " ideal model delta sigma weight residual 121.48 129.66 -8.18 2.04e+00 2.40e-01 1.61e+01 ... (remaining 6337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 2634 14.52 - 29.04: 108 29.04 - 43.56: 34 43.56 - 58.08: 3 58.08 - 72.60: 7 Dihedral angle restraints: 2786 sinusoidal: 1086 harmonic: 1700 Sorted by residual: dihedral pdb=" CA ASP B 223 " pdb=" C ASP B 223 " pdb=" N LYS B 224 " pdb=" CA LYS B 224 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP A 223 " pdb=" C ASP A 223 " pdb=" N LYS A 224 " pdb=" CA LYS A 224 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA TYR A 245 " pdb=" C TYR A 245 " pdb=" N GLU A 246 " pdb=" CA GLU A 246 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 2783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 559 0.055 - 0.109: 141 0.109 - 0.164: 24 0.164 - 0.218: 2 0.218 - 0.273: 4 Chirality restraints: 730 Sorted by residual: chirality pdb=" CA LEU A 172 " pdb=" N LEU A 172 " pdb=" C LEU A 172 " pdb=" CB LEU A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA LEU B 172 " pdb=" N LEU B 172 " pdb=" C LEU B 172 " pdb=" CB LEU B 172 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ASN A 152 " pdb=" N ASN A 152 " pdb=" C ASN A 152 " pdb=" CB ASN A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 727 not shown) Planarity restraints: 798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 172 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 173 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 172 " -0.036 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO B 173 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 7 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A 8 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 8 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 8 " 0.027 5.00e-02 4.00e+02 ... (remaining 795 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1337 2.82 - 3.34: 4039 3.34 - 3.86: 7068 3.86 - 4.38: 7543 4.38 - 4.90: 13049 Nonbonded interactions: 33036 Sorted by model distance: nonbonded pdb=" O TYR A 81 " pdb=" OG1 THR A 84 " model vdw 2.300 2.440 nonbonded pdb=" O TYR B 81 " pdb=" OG1 THR B 84 " model vdw 2.301 2.440 nonbonded pdb=" O LEU A 124 " pdb=" OG SER A 127 " model vdw 2.388 2.440 nonbonded pdb=" O LEU B 124 " pdb=" OG SER B 127 " model vdw 2.390 2.440 nonbonded pdb=" O HIS A 50 " pdb=" OG SER A 53 " model vdw 2.461 2.440 ... (remaining 33031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.460 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: 2.180 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.400 Find NCS groups from input model: 0.270 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 0.055 4676 Z= 0.420 Angle : 0.931 11.310 6342 Z= 0.495 Chirality : 0.053 0.273 730 Planarity : 0.008 0.054 798 Dihedral : 10.321 72.601 1686 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.41 % Allowed : 1.23 % Favored : 98.35 % 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: -2.40 (0.29), residues: 552 helix: -1.14 (0.24), residues: 304 sheet: -1.41 (0.79), residues: 28 loop : -2.13 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 82 HIS 0.007 0.002 HIS B 157 PHE 0.019 0.003 PHE A 153 TYR 0.032 0.003 TYR B 199 ARG 0.011 0.001 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.1476 time to fit residues: 24.5879 Evaluate side-chains 41 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 196 GLN A 287 GLN B 128 GLN B 196 GLN B 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4676 Z= 0.182 Angle : 0.580 6.907 6342 Z= 0.285 Chirality : 0.040 0.136 730 Planarity : 0.005 0.036 798 Dihedral : 4.766 17.272 638 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: -0.04 (0.35), residues: 552 helix: 0.99 (0.29), residues: 318 sheet: -0.48 (0.87), residues: 28 loop : -1.59 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 119 HIS 0.005 0.001 HIS B 50 PHE 0.011 0.001 PHE B 153 TYR 0.015 0.001 TYR A 261 ARG 0.002 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1175 time to fit residues: 12.5041 Evaluate side-chains 38 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4676 Z= 0.166 Angle : 0.546 6.164 6342 Z= 0.266 Chirality : 0.040 0.187 730 Planarity : 0.004 0.029 798 Dihedral : 4.374 14.975 638 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.37), residues: 552 helix: 1.76 (0.30), residues: 318 sheet: -0.15 (0.88), residues: 28 loop : -1.19 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 119 HIS 0.003 0.001 HIS B 157 PHE 0.007 0.001 PHE B 153 TYR 0.013 0.001 TYR A 199 ARG 0.002 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1427 time to fit residues: 10.8075 Evaluate side-chains 33 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.522 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4676 Z= 0.159 Angle : 0.524 5.803 6342 Z= 0.252 Chirality : 0.039 0.127 730 Planarity : 0.003 0.026 798 Dihedral : 4.146 14.930 638 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: 1.24 (0.37), residues: 552 helix: 2.02 (0.30), residues: 318 sheet: -0.12 (0.89), residues: 28 loop : -0.99 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 119 HIS 0.003 0.001 HIS B 50 PHE 0.007 0.001 PHE B 105 TYR 0.011 0.001 TYR A 199 ARG 0.001 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1493 time to fit residues: 11.8116 Evaluate side-chains 32 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 0.0170 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4676 Z= 0.295 Angle : 0.634 6.136 6342 Z= 0.305 Chirality : 0.041 0.130 730 Planarity : 0.004 0.028 798 Dihedral : 4.466 14.775 638 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: 1.08 (0.38), residues: 552 helix: 1.86 (0.30), residues: 320 sheet: -0.84 (0.70), residues: 54 loop : -0.87 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 119 HIS 0.004 0.001 HIS B 157 PHE 0.012 0.002 PHE A 269 TYR 0.017 0.002 TYR B 199 ARG 0.004 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.523 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1223 time to fit residues: 8.9439 Evaluate side-chains 26 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 218 ASN B 50 HIS B 218 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4676 Z= 0.124 Angle : 0.520 6.097 6342 Z= 0.252 Chirality : 0.039 0.194 730 Planarity : 0.003 0.035 798 Dihedral : 4.038 15.324 638 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 1.51 (0.38), residues: 552 helix: 2.17 (0.31), residues: 318 sheet: -0.29 (0.92), residues: 28 loop : -0.69 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 119 HIS 0.007 0.001 HIS B 50 PHE 0.006 0.001 PHE A 153 TYR 0.009 0.001 TYR A 261 ARG 0.004 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.485 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1207 time to fit residues: 10.8721 Evaluate side-chains 34 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.531 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 55 optimal weight: 0.2980 chunk 34 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4676 Z= 0.223 Angle : 0.562 5.621 6342 Z= 0.272 Chirality : 0.039 0.161 730 Planarity : 0.003 0.027 798 Dihedral : 4.131 15.227 638 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.38), residues: 552 helix: 1.98 (0.31), residues: 320 sheet: -0.70 (0.76), residues: 46 loop : -0.85 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 119 HIS 0.003 0.001 HIS B 157 PHE 0.008 0.001 PHE B 269 TYR 0.013 0.001 TYR A 199 ARG 0.003 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.478 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1272 time to fit residues: 8.7525 Evaluate side-chains 26 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4676 Z= 0.239 Angle : 0.586 5.681 6342 Z= 0.284 Chirality : 0.040 0.149 730 Planarity : 0.003 0.027 798 Dihedral : 4.203 14.956 638 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: 1.13 (0.38), residues: 552 helix: 1.92 (0.31), residues: 322 sheet: -0.80 (0.76), residues: 46 loop : -0.96 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 119 HIS 0.004 0.001 HIS B 157 PHE 0.009 0.001 PHE A 269 TYR 0.013 0.001 TYR B 199 ARG 0.002 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1257 time to fit residues: 8.3525 Evaluate side-chains 25 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 52.5692 > 50: distance: 34 - 94: 4.800 distance: 42 - 97: 7.926 distance: 94 - 95: 3.889 distance: 95 - 96: 4.946 distance: 95 - 98: 4.985 distance: 96 - 103: 9.284 distance: 98 - 99: 3.135 distance: 99 - 100: 6.246 distance: 100 - 101: 8.054 distance: 100 - 102: 4.989 distance: 104 - 105: 5.528 distance: 104 - 107: 6.285 distance: 105 - 106: 3.550 distance: 105 - 115: 8.764 distance: 107 - 108: 3.688 distance: 108 - 109: 8.262 distance: 108 - 110: 6.553 distance: 109 - 111: 4.557 distance: 110 - 112: 6.047 distance: 111 - 113: 7.306 distance: 112 - 113: 4.553 distance: 113 - 114: 10.195 distance: 115 - 116: 13.253 distance: 116 - 117: 11.266 distance: 116 - 119: 19.774 distance: 117 - 118: 22.281 distance: 117 - 120: 7.137 distance: 120 - 121: 9.395 distance: 121 - 122: 10.564 distance: 121 - 124: 24.196 distance: 122 - 123: 13.159 distance: 122 - 127: 6.593 distance: 124 - 125: 16.797 distance: 124 - 126: 11.682 distance: 127 - 128: 10.542 distance: 127 - 133: 19.724 distance: 128 - 129: 3.145 distance: 128 - 131: 11.194 distance: 129 - 130: 16.860 distance: 129 - 134: 25.647 distance: 130 - 158: 25.974 distance: 131 - 132: 7.746 distance: 132 - 133: 17.673 distance: 134 - 135: 37.288 distance: 135 - 136: 14.124 distance: 135 - 138: 16.511 distance: 136 - 137: 9.095 distance: 136 - 142: 11.566 distance: 137 - 166: 19.661 distance: 138 - 139: 32.524 distance: 139 - 140: 34.447 distance: 139 - 141: 21.297 distance: 142 - 143: 15.677 distance: 143 - 144: 8.412 distance: 143 - 146: 20.064 distance: 144 - 145: 3.644 distance: 144 - 151: 4.075 distance: 145 - 177: 11.344 distance: 146 - 147: 5.062 distance: 147 - 148: 18.203 distance: 148 - 149: 20.485 distance: 148 - 150: 13.720 distance: 151 - 152: 4.642 distance: 152 - 153: 8.416 distance: 152 - 155: 6.455 distance: 154 - 182: 3.402 distance: 155 - 156: 4.880 distance: 155 - 157: 5.761 distance: 158 - 159: 4.161 distance: 159 - 162: 4.732 distance: 160 - 166: 3.179 distance: 163 - 164: 6.185 distance: 163 - 165: 9.870 distance: 166 - 167: 4.702 distance: 167 - 168: 4.946 distance: 167 - 170: 7.361 distance: 168 - 169: 3.939 distance: 168 - 177: 5.082 distance: 169 - 196: 8.587 distance: 170 - 171: 8.089 distance: 171 - 172: 4.401 distance: 171 - 173: 9.459 distance: 172 - 174: 7.840 distance: 173 - 175: 6.026 distance: 174 - 176: 7.445 distance: 175 - 176: 3.387