Starting phenix.real_space_refine on Sun Mar 10 19:54:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/03_2024/6nt5_0502_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/03_2024/6nt5_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_0502/03_2024/6nt5_0502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/03_2024/6nt5_0502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/03_2024/6nt5_0502_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt5_0502/03_2024/6nt5_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.93, 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: 1.84 Conformation dependent library (CDL) restraints added in 834.1 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: 1.22 Time building geometry restraints manager: 1.99 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: 0.420 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: 2.140 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.920 Find NCS groups from input model: 0.240 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- 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 : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.8973 (t0) cc_final: 0.8579 (t0) REVERT: A 93 LEU cc_start: 0.8599 (mt) cc_final: 0.8245 (pp) REVERT: A 119 TRP cc_start: 0.7263 (p90) cc_final: 0.7051 (p90) REVERT: A 183 ASN cc_start: 0.7717 (m-40) cc_final: 0.6849 (p0) REVERT: A 223 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: B 61 ASN cc_start: 0.8981 (t0) cc_final: 0.8585 (t0) REVERT: B 93 LEU cc_start: 0.8635 (mt) cc_final: 0.8278 (pp) REVERT: B 104 TYR cc_start: 0.7430 (t80) cc_final: 0.7212 (t80) REVERT: B 154 ASN cc_start: 0.8612 (t0) cc_final: 0.8310 (p0) REVERT: B 183 ASN cc_start: 0.7659 (m-40) cc_final: 0.6804 (p0) REVERT: B 223 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.7878 (m-30) outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.1483 time to fit residues: 24.5393 Evaluate side-chains 51 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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: 0.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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: 0.8154 moved from start: 0.2569 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= 0.152 Angle : 0.552 6.812 6342 Z= 0.273 Chirality : 0.040 0.134 730 Planarity : 0.005 0.037 798 Dihedral : 4.587 17.318 638 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: 0.03 (0.35), residues: 552 helix: 1.03 (0.29), residues: 318 sheet: -0.22 (0.86), residues: 28 loop : -1.54 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 161 HIS 0.005 0.001 HIS B 50 PHE 0.009 0.001 PHE B 153 TYR 0.014 0.001 TYR B 199 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 87 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 ASN cc_start: 0.7869 (m-40) cc_final: 0.7030 (p0) REVERT: B 155 VAL cc_start: 0.9109 (t) cc_final: 0.8709 (p) REVERT: B 183 ASN cc_start: 0.7747 (m-40) cc_final: 0.6867 (p0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1134 time to fit residues: 13.9466 Evaluate side-chains 43 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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: 7.9990 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3155 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= 0.128 Angle : 0.505 6.066 6342 Z= 0.247 Chirality : 0.039 0.190 730 Planarity : 0.004 0.029 798 Dihedral : 4.090 14.912 638 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 1.04 (0.36), residues: 552 helix: 1.84 (0.30), residues: 318 sheet: 0.18 (0.87), residues: 28 loop : -1.09 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 161 HIS 0.004 0.001 HIS B 50 PHE 0.007 0.001 PHE A 279 TYR 0.013 0.001 TYR A 261 ARG 0.001 0.000 ARG A 293 *********************** 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 62 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 VAL cc_start: 0.8918 (t) cc_final: 0.8606 (p) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1185 time to fit residues: 10.4200 Evaluate side-chains 38 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 0.0370 chunk 56 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- 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: 0.8127 moved from start: 0.3387 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= 0.123 Angle : 0.487 5.759 6342 Z= 0.234 Chirality : 0.038 0.133 730 Planarity : 0.003 0.025 798 Dihedral : 3.886 14.994 638 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: 1.56 (0.37), residues: 552 helix: 2.20 (0.30), residues: 322 sheet: 0.27 (0.86), residues: 28 loop : -0.82 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 119 HIS 0.004 0.001 HIS B 50 PHE 0.007 0.001 PHE A 279 TYR 0.010 0.001 TYR A 261 ARG 0.001 0.000 ARG A 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 62 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 VAL cc_start: 0.8913 (t) cc_final: 0.8546 (p) REVERT: B 208 VAL cc_start: 0.9203 (t) cc_final: 0.8989 (t) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1328 time to fit residues: 11.3554 Evaluate side-chains 39 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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: 0.0060 chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.4980 chunk 50 optimal weight: 8.9990 chunk 14 optimal weight: 0.0070 chunk 18 optimal weight: 0.0770 chunk 11 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.1270 ------------------------------------------------------------------------------- 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: 0.8083 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4676 Z= 0.104 Angle : 0.480 6.168 6342 Z= 0.226 Chirality : 0.037 0.120 730 Planarity : 0.003 0.025 798 Dihedral : 3.651 15.213 638 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.38), residues: 552 helix: 2.30 (0.30), residues: 324 sheet: 0.31 (0.85), residues: 28 loop : -0.62 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 161 HIS 0.006 0.001 HIS B 50 PHE 0.007 0.001 PHE B 105 TYR 0.009 0.001 TYR B 261 ARG 0.001 0.000 ARG B 83 *********************** 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 61 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9097 (mm) cc_final: 0.8895 (tt) REVERT: B 155 VAL cc_start: 0.8864 (t) cc_final: 0.8534 (p) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1152 time to fit residues: 10.1046 Evaluate side-chains 39 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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: 7.9990 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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: 0.8191 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4676 Z= 0.199 Angle : 0.537 5.829 6342 Z= 0.258 Chirality : 0.040 0.202 730 Planarity : 0.003 0.025 798 Dihedral : 3.873 15.287 638 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % 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: 1.87 (0.38), residues: 552 helix: 2.38 (0.31), residues: 322 sheet: 0.34 (0.90), residues: 28 loop : -0.55 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 161 HIS 0.007 0.001 HIS B 332 PHE 0.008 0.001 PHE A 269 TYR 0.011 0.001 TYR A 199 ARG 0.002 0.000 ARG B 197 *********************** 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 54 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.594 Fit side-chains REVERT: A 100 LEU cc_start: 0.9133 (mm) cc_final: 0.8888 (tt) REVERT: B 155 VAL cc_start: 0.9040 (t) cc_final: 0.8729 (p) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1192 time to fit residues: 9.2780 Evaluate side-chains 31 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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: 7.9990 chunk 47 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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: 0.8182 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4676 Z= 0.176 Angle : 0.509 5.689 6342 Z= 0.246 Chirality : 0.039 0.152 730 Planarity : 0.003 0.024 798 Dihedral : 3.866 14.934 638 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: 1.94 (0.38), residues: 552 helix: 2.34 (0.30), residues: 328 sheet: 0.40 (0.93), residues: 28 loop : -0.40 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 119 HIS 0.006 0.001 HIS B 332 PHE 0.006 0.001 PHE B 269 TYR 0.011 0.001 TYR B 199 ARG 0.002 0.000 ARG A 197 *********************** 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 57 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.551 Fit side-chains REVERT: A 100 LEU cc_start: 0.9130 (mm) cc_final: 0.8881 (tt) REVERT: A 155 VAL cc_start: 0.9097 (t) cc_final: 0.8738 (p) REVERT: B 155 VAL cc_start: 0.9014 (t) cc_final: 0.8701 (p) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1183 time to fit residues: 9.7968 Evaluate side-chains 30 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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: 6.9990 chunk 5 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 0.4980 chunk 48 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.0470 chunk 15 optimal weight: 0.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS B 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4041 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= 0.120 Angle : 0.483 6.109 6342 Z= 0.231 Chirality : 0.038 0.130 730 Planarity : 0.003 0.024 798 Dihedral : 3.665 15.090 638 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 2.12 (0.39), residues: 552 helix: 2.51 (0.31), residues: 326 sheet: 0.62 (0.94), residues: 28 loop : -0.38 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 119 HIS 0.007 0.001 HIS B 50 PHE 0.004 0.001 PHE B 153 TYR 0.009 0.001 TYR B 199 ARG 0.003 0.000 ARG B 293 *********************** 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 60 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.556 Fit side-chains REVERT: A 100 LEU cc_start: 0.9124 (mm) cc_final: 0.8883 (tt) REVERT: A 155 VAL cc_start: 0.9039 (t) cc_final: 0.8681 (p) REVERT: B 155 VAL cc_start: 0.8987 (t) cc_final: 0.8674 (p) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1223 time to fit residues: 10.5598 Evaluate side-chains 31 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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: 4.9990 chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 55 optimal weight: 0.0870 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 0.0870 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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: 0.8114 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 4676 Z= 0.109 Angle : 0.501 6.910 6342 Z= 0.235 Chirality : 0.037 0.127 730 Planarity : 0.003 0.025 798 Dihedral : 3.562 14.712 638 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.77 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: 2.10 (0.39), residues: 552 helix: 2.48 (0.31), residues: 326 sheet: 0.95 (0.95), residues: 28 loop : -0.41 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 161 HIS 0.007 0.001 HIS B 50 PHE 0.004 0.001 PHE B 279 TYR 0.009 0.001 TYR B 199 ARG 0.002 0.000 ARG A 180 *********************** 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 60 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9117 (mm) cc_final: 0.8889 (tt) REVERT: A 155 VAL cc_start: 0.9013 (t) cc_final: 0.8687 (p) REVERT: B 155 VAL cc_start: 0.8988 (t) cc_final: 0.8672 (p) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1131 time to fit residues: 9.7080 Evaluate side-chains 32 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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: 1.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 14 optimal weight: 0.0270 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.9640 ------------------------------------------------------------------------------- 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: 0.8120 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4676 Z= 0.120 Angle : 0.493 6.891 6342 Z= 0.234 Chirality : 0.038 0.128 730 Planarity : 0.003 0.028 798 Dihedral : 3.559 14.965 638 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 2.10 (0.39), residues: 552 helix: 2.50 (0.31), residues: 326 sheet: 0.97 (0.94), residues: 28 loop : -0.46 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 161 HIS 0.006 0.001 HIS B 50 PHE 0.005 0.001 PHE B 279 TYR 0.009 0.001 TYR B 199 ARG 0.002 0.000 ARG A 180 ********************** 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 59 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9123 (mm) cc_final: 0.8901 (tt) REVERT: A 155 VAL cc_start: 0.9021 (t) cc_final: 0.8648 (p) REVERT: B 119 TRP cc_start: 0.7458 (p90) cc_final: 0.6653 (p90) REVERT: B 155 VAL cc_start: 0.9004 (t) cc_final: 0.8681 (p) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1334 time to fit residues: 10.8025 Evaluate side-chains 27 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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: 4.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 40 optimal weight: 0.0270 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS B 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.077762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.064671 restraints weight = 18986.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.066389 restraints weight = 10521.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.067527 restraints weight = 7011.857| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4676 Z= 0.323 Angle : 0.668 6.325 6342 Z= 0.323 Chirality : 0.043 0.143 730 Planarity : 0.004 0.038 798 Dihedral : 4.139 14.829 638 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % 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: 1.47 (0.37), residues: 552 helix: 2.01 (0.30), residues: 324 sheet: 0.60 (0.96), residues: 28 loop : -0.71 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 119 HIS 0.005 0.001 HIS B 332 PHE 0.013 0.002 PHE B 269 TYR 0.016 0.002 TYR A 261 ARG 0.007 0.001 ARG B 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1144.81 seconds wall clock time: 21 minutes 26.87 seconds (1286.87 seconds total)