Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:40:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/11_2022/6nt5_0502_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/11_2022/6nt5_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_0502/11_2022/6nt5_0502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/11_2022/6nt5_0502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/11_2022/6nt5_0502_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/11_2022/6nt5_0502_neut.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-dev-4778/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: 3.14, per 1000 atoms: 0.68 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: 1.82 Conformation dependent library (CDL) restraints added in 697.4 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: 0.23 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: 1.12 Time building geometry restraints manager: 1.97 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 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. 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: 0.340 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: 0.010 Extract box with map and model: 2.330 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 16.390 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.41 % 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 *********************** 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 : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.1387 time to fit residues: 23.0518 Evaluate side-chains 41 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7270 ------------------------------------------------------------------------------- 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: 0.8166 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 : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1247 time to fit residues: 13.2579 Evaluate side-chains 38 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7513 ------------------------------------------------------------------------------- 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: 0.0980 chunk 16 optimal weight: 0.0470 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.6080 ------------------------------------------------------------------------------- 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: 0.8103 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 4676 Z= 0.119 Angle : 0.511 5.772 6342 Z= 0.248 Chirality : 0.039 0.180 730 Planarity : 0.004 0.028 798 Dihedral : 4.179 15.075 638 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.00 % 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: 1.00 (0.37), residues: 552 helix: 1.83 (0.30), residues: 318 sheet: 0.18 (0.88), residues: 28 loop : -1.16 (0.42), residues: 206 *********************** 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 66 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1254 time to fit residues: 11.5798 Evaluate side-chains 36 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7363 ------------------------------------------------------------------------------- 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: 8.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 4676 Z= 0.172 Angle : 0.527 5.874 6342 Z= 0.255 Chirality : 0.039 0.127 730 Planarity : 0.003 0.025 798 Dihedral : 4.068 14.917 638 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 0.00 % 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: 1.35 (0.37), residues: 552 helix: 2.06 (0.31), residues: 318 sheet: 0.48 (0.88), residues: 28 loop : -0.94 (0.43), residues: 206 *********************** 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 54 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1550 time to fit residues: 11.3124 Evaluate side-chains 31 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7626 ------------------------------------------------------------------------------- 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: 5.9990 chunk 50 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.0040 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4676 Z= 0.223 Angle : 0.571 6.189 6342 Z= 0.274 Chirality : 0.040 0.128 730 Planarity : 0.003 0.025 798 Dihedral : 4.257 14.992 638 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.00 % 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: 1.38 (0.38), residues: 552 helix: 1.96 (0.30), residues: 320 sheet: 0.46 (0.98), residues: 28 loop : -0.72 (0.45), residues: 204 *********************** 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 52 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.579 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1335 time to fit residues: 9.8342 Evaluate side-chains 31 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8206 ------------------------------------------------------------------------------- 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: 5.9990 chunk 56 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 0.0470 chunk 29 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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: 0.8196 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 : 0.003 0.031 4676 Z= 0.204 Angle : 0.556 5.727 6342 Z= 0.268 Chirality : 0.040 0.192 730 Planarity : 0.003 0.026 798 Dihedral : 4.148 14.682 638 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.00 % 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: 1.40 (0.38), residues: 552 helix: 2.02 (0.30), residues: 320 sheet: -0.31 (0.73), residues: 54 loop : -0.66 (0.51), residues: 178 *********************** 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 51 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.579 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1156 time to fit residues: 8.6790 Evaluate side-chains 32 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7575 ------------------------------------------------------------------------------- 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: 6.9990 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 0.2980 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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: 0.8157 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 4676 Z= 0.145 Angle : 0.504 6.030 6342 Z= 0.243 Chirality : 0.038 0.144 730 Planarity : 0.003 0.027 798 Dihedral : 3.953 14.769 638 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.00 % 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: 1.75 (0.38), residues: 552 helix: 2.18 (0.31), residues: 324 sheet: 0.63 (1.00), residues: 28 loop : -0.47 (0.47), residues: 200 *********************** 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 56 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.631 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1257 time to fit residues: 9.9958 Evaluate side-chains 29 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7690 ------------------------------------------------------------------------------- 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: 0.8980 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 50 optimal weight: 0.0040 chunk 53 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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: 0.8117 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 4676 Z= 0.113 Angle : 0.493 6.294 6342 Z= 0.236 Chirality : 0.038 0.125 730 Planarity : 0.003 0.027 798 Dihedral : 3.751 14.744 638 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 0.00 % 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: 1.88 (0.39), residues: 552 helix: 2.27 (0.31), residues: 326 sheet: 0.81 (0.99), residues: 28 loop : -0.45 (0.48), residues: 198 *********************** 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 54 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.583 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1212 time to fit residues: 9.3569 Evaluate side-chains 33 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.8139 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 4676 Z= 0.150 Angle : 0.530 6.161 6342 Z= 0.255 Chirality : 0.038 0.132 730 Planarity : 0.003 0.035 798 Dihedral : 3.791 14.802 638 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.00 % 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: 1.79 (0.38), residues: 552 helix: 2.23 (0.30), residues: 324 sheet: 0.97 (0.99), residues: 28 loop : -0.55 (0.46), residues: 200 *********************** REFINEMENT MACRO_CYCLE 9 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 52 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1086 time to fit residues: 8.3488 Evaluate side-chains 32 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 42 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 4676 Z= 0.130 Angle : 0.519 6.320 6342 Z= 0.245 Chirality : 0.038 0.131 730 Planarity : 0.003 0.027 798 Dihedral : 3.744 14.720 638 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.39), residues: 552 helix: 2.32 (0.31), residues: 326 sheet: 1.02 (0.98), residues: 28 loop : -0.47 (0.47), residues: 198 ********************** REFINEMENT MACRO_CYCLE 10 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 53 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1150 time to fit residues: 8.8933 Evaluate side-chains 32 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 40 optimal weight: 0.0980 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 36 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.080808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.067787 restraints weight = 18868.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.069534 restraints weight = 10439.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.070739 restraints weight = 6973.237| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 4676 Z= 0.137 Angle : 0.528 6.394 6342 Z= 0.249 Chirality : 0.038 0.128 730 Planarity : 0.003 0.027 798 Dihedral : 3.769 16.100 638 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.00 % 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: 1.95 (0.39), residues: 552 helix: 2.33 (0.31), residues: 326 sheet: 1.15 (0.99), residues: 28 loop : -0.48 (0.47), residues: 198 =============================================================================== Job complete usr+sys time: 1089.88 seconds wall clock time: 20 minutes 58.68 seconds (1258.68 seconds total)