Starting phenix.real_space_refine on Fri Aug 2 17:53:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuz_42602/08_2024/8uuz_42602.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuz_42602/08_2024/8uuz_42602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuz_42602/08_2024/8uuz_42602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuz_42602/08_2024/8uuz_42602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuz_42602/08_2024/8uuz_42602.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuz_42602/08_2024/8uuz_42602.cif" } resolution = 3.77 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2228 atoms to isotropic. 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 6 5.16 5 C 1426 2.51 5 N 372 2.21 5 O 454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 2258 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1129 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1129 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 2.40, per 1000 atoms: 1.06 Number of scatterers: 2258 At special positions: 0 Unit cell: (51.282, 68.598, 65.934, 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 6 16.00 O 454 8.00 N 372 7.00 C 1426 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: 0.76 Conformation dependent library (CDL) restraints added in 392.1 milliseconds 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 560 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 4 sheets defined 46.3% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.557A pdb=" N ILE A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 43 removed outlier: 3.983A pdb=" N GLY A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 67 removed outlier: 4.129A pdb=" N LYS A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'B' and resid 9 through 22 removed outlier: 3.828A pdb=" N ASN B 19 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 43 removed outlier: 3.970A pdb=" N GLY B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG B 43 " --> pdb=" O PHE B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 removed outlier: 4.149A pdb=" N LYS B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 152 through 161 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 79 83 hydrogen bonds defined for protein. 243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.47 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 772 1.34 - 1.46: 343 1.46 - 1.57: 1165 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 2292 Sorted by residual: bond pdb=" CG LEU A 49 " pdb=" CD1 LEU A 49 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.46e+00 bond pdb=" CA SER A 51 " pdb=" C SER A 51 " ideal model delta sigma weight residual 1.529 1.512 0.017 1.44e-02 4.82e+03 1.39e+00 bond pdb=" CA SER B 51 " pdb=" C SER B 51 " ideal model delta sigma weight residual 1.529 1.513 0.016 1.44e-02 4.82e+03 1.30e+00 bond pdb=" C SER B 51 " pdb=" N TRP B 52 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.26e-02 6.30e+03 1.23e+00 bond pdb=" C SER A 51 " pdb=" N TRP A 52 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.26e-02 6.30e+03 1.21e+00 ... (remaining 2287 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 64 107.14 - 113.86: 1325 113.86 - 120.57: 830 120.57 - 127.29: 873 127.29 - 134.00: 18 Bond angle restraints: 3110 Sorted by residual: angle pdb=" C THR B 73 " pdb=" CA THR B 73 " pdb=" CB THR B 73 " ideal model delta sigma weight residual 117.23 110.60 6.63 1.36e+00 5.41e-01 2.38e+01 angle pdb=" C THR A 73 " pdb=" CA THR A 73 " pdb=" CB THR A 73 " ideal model delta sigma weight residual 117.23 110.64 6.59 1.36e+00 5.41e-01 2.35e+01 angle pdb=" N SER A 51 " pdb=" CA SER A 51 " pdb=" C SER A 51 " ideal model delta sigma weight residual 109.65 115.26 -5.61 1.56e+00 4.11e-01 1.29e+01 angle pdb=" CA THR A 73 " pdb=" C THR A 73 " pdb=" N SER A 74 " ideal model delta sigma weight residual 119.98 116.95 3.03 8.50e-01 1.38e+00 1.27e+01 angle pdb=" CA THR B 73 " pdb=" C THR B 73 " pdb=" N SER B 74 " ideal model delta sigma weight residual 119.98 117.05 2.93 8.50e-01 1.38e+00 1.19e+01 ... (remaining 3105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 1183 11.82 - 23.65: 118 23.65 - 35.47: 45 35.47 - 47.29: 17 47.29 - 59.12: 7 Dihedral angle restraints: 1370 sinusoidal: 508 harmonic: 862 Sorted by residual: dihedral pdb=" N LEU A 103 " pdb=" CA LEU A 103 " pdb=" CB LEU A 103 " pdb=" CG LEU A 103 " ideal model delta sinusoidal sigma weight residual -180.00 -120.88 -59.12 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU B 103 " pdb=" CA LEU B 103 " pdb=" CB LEU B 103 " pdb=" CG LEU B 103 " ideal model delta sinusoidal sigma weight residual 180.00 -121.96 -58.04 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LEU B 54 " pdb=" CA LEU B 54 " pdb=" CB LEU B 54 " pdb=" CG LEU B 54 " ideal model delta sinusoidal sigma weight residual -60.00 -114.59 54.59 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 1367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 215 0.031 - 0.062: 94 0.062 - 0.093: 37 0.093 - 0.123: 16 0.123 - 0.154: 4 Chirality restraints: 366 Sorted by residual: chirality pdb=" CA ILE B 77 " pdb=" N ILE B 77 " pdb=" C ILE B 77 " pdb=" CB ILE B 77 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE A 77 " pdb=" N ILE A 77 " pdb=" C ILE A 77 " pdb=" CB ILE A 77 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ASN B 13 " pdb=" N ASN B 13 " pdb=" C ASN B 13 " pdb=" CB ASN B 13 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 363 not shown) Planarity restraints: 406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 54 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO B 55 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 54 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 55 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 18 " -0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C ASP A 18 " 0.019 2.00e-02 2.50e+03 pdb=" O ASP A 18 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN A 19 " -0.006 2.00e-02 2.50e+03 ... (remaining 403 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 338 2.75 - 3.29: 2633 3.29 - 3.83: 4288 3.83 - 4.36: 5025 4.36 - 4.90: 7571 Nonbonded interactions: 19855 Sorted by model distance: nonbonded pdb=" O ILE A 88 " pdb=" NZ LYS A 92 " model vdw 2.213 3.120 nonbonded pdb=" O ILE B 88 " pdb=" NZ LYS B 92 " model vdw 2.214 3.120 nonbonded pdb=" OD2 ASP B 28 " pdb=" OH TYR B 45 " model vdw 2.228 3.040 nonbonded pdb=" ND2 ASN A 13 " pdb=" O SER A 30 " model vdw 2.258 3.120 nonbonded pdb=" OD2 ASP A 28 " pdb=" OH TYR A 45 " model vdw 2.265 3.040 ... (remaining 19850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.720 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3512 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 : 0.003 0.040 2292 Z= 0.222 Angle : 0.730 7.192 3110 Z= 0.422 Chirality : 0.045 0.154 366 Planarity : 0.003 0.033 406 Dihedral : 13.057 59.116 810 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 38.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 12.61 % Allowed : 9.57 % Favored : 77.83 % 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: -1.81 (0.48), residues: 288 helix: 0.26 (0.48), residues: 116 sheet: -3.95 (0.62), residues: 34 loop : -1.70 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 52 HIS 0.002 0.001 HIS A 44 PHE 0.012 0.001 PHE B 98 TYR 0.008 0.001 TYR B 140 ARG 0.002 0.000 ARG B 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 65 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 VAL cc_start: 0.7274 (OUTLIER) cc_final: 0.6450 (t) REVERT: B 99 VAL cc_start: 0.6945 (OUTLIER) cc_final: 0.6277 (t) outliers start: 29 outliers final: 7 residues processed: 86 average time/residue: 0.1802 time to fit residues: 17.4497 Evaluate side-chains 62 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 0.0030 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 64 ASN B 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3476 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2292 Z= 0.228 Angle : 0.805 9.724 3110 Z= 0.403 Chirality : 0.051 0.262 366 Planarity : 0.006 0.052 406 Dihedral : 9.027 46.915 330 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 35.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 5.22 % Allowed : 27.83 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.47), residues: 288 helix: 0.26 (0.46), residues: 120 sheet: -3.46 (0.76), residues: 34 loop : -1.96 (0.50), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP A 52 HIS 0.001 0.001 HIS A 68 PHE 0.019 0.002 PHE B 152 TYR 0.006 0.001 TYR A 45 ARG 0.003 0.001 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 VAL cc_start: 0.7091 (OUTLIER) cc_final: 0.6866 (t) REVERT: A 109 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5495 (tp) REVERT: B 98 PHE cc_start: 0.4669 (OUTLIER) cc_final: 0.3708 (t80) REVERT: B 109 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5530 (tp) outliers start: 12 outliers final: 5 residues processed: 62 average time/residue: 0.2016 time to fit residues: 14.0887 Evaluate side-chains 59 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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: 0.3483 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2292 Z= 0.222 Angle : 0.725 8.576 3110 Z= 0.375 Chirality : 0.048 0.189 366 Planarity : 0.005 0.056 406 Dihedral : 8.082 43.535 323 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 34.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 8.70 % Allowed : 22.61 % Favored : 68.70 % 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: -1.98 (0.46), residues: 288 helix: -0.05 (0.43), residues: 134 sheet: -3.27 (0.76), residues: 34 loop : -2.12 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 52 HIS 0.001 0.000 HIS A 68 PHE 0.020 0.002 PHE A 152 TYR 0.007 0.001 TYR B 140 ARG 0.008 0.001 ARG B 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5406 (tp) REVERT: B 98 PHE cc_start: 0.4576 (OUTLIER) cc_final: 0.3629 (t80) REVERT: B 109 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5437 (tp) outliers start: 20 outliers final: 10 residues processed: 64 average time/residue: 0.1875 time to fit residues: 13.5739 Evaluate side-chains 61 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 0.0980 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.3382 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2292 Z= 0.202 Angle : 0.680 7.501 3110 Z= 0.357 Chirality : 0.048 0.183 366 Planarity : 0.005 0.054 406 Dihedral : 7.890 43.192 322 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 29.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 8.26 % Allowed : 23.48 % Favored : 68.26 % 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: -1.92 (0.47), residues: 288 helix: -0.27 (0.42), residues: 136 sheet: -2.71 (0.87), residues: 34 loop : -1.93 (0.52), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 52 HIS 0.002 0.001 HIS A 68 PHE 0.012 0.001 PHE A 98 TYR 0.005 0.001 TYR B 140 ARG 0.007 0.001 ARG B 2 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 52 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.5683 (OUTLIER) cc_final: 0.5067 (tp) REVERT: B 98 PHE cc_start: 0.4241 (OUTLIER) cc_final: 0.3111 (t80) REVERT: B 109 LEU cc_start: 0.5635 (OUTLIER) cc_final: 0.5242 (tp) outliers start: 19 outliers final: 10 residues processed: 64 average time/residue: 0.1792 time to fit residues: 13.0421 Evaluate side-chains 62 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 5 optimal weight: 0.0000 chunk 17 optimal weight: 0.9980 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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: 0.3281 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2292 Z= 0.193 Angle : 0.660 6.391 3110 Z= 0.347 Chirality : 0.047 0.155 366 Planarity : 0.005 0.059 406 Dihedral : 7.352 42.457 320 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 8.26 % Allowed : 27.39 % Favored : 64.35 % 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: -1.89 (0.47), residues: 288 helix: -0.20 (0.43), residues: 136 sheet: -2.66 (0.88), residues: 34 loop : -2.00 (0.52), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 52 HIS 0.002 0.000 HIS B 68 PHE 0.012 0.001 PHE A 152 TYR 0.007 0.001 TYR B 45 ARG 0.004 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 48 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 0 MET cc_start: 0.5613 (tpp) cc_final: 0.4273 (tpt) REVERT: A 107 ILE cc_start: 0.5954 (pt) cc_final: 0.5007 (pt) REVERT: B 49 LEU cc_start: 0.2484 (OUTLIER) cc_final: 0.1854 (mm) REVERT: B 98 PHE cc_start: 0.3742 (OUTLIER) cc_final: 0.2728 (t80) REVERT: B 109 LEU cc_start: 0.5666 (OUTLIER) cc_final: 0.5279 (tp) outliers start: 19 outliers final: 10 residues processed: 60 average time/residue: 0.1917 time to fit residues: 12.9993 Evaluate side-chains 59 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 46 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 27 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.3425 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2292 Z= 0.222 Angle : 0.699 7.466 3110 Z= 0.368 Chirality : 0.047 0.161 366 Planarity : 0.005 0.057 406 Dihedral : 7.468 48.049 320 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 33.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 6.96 % Allowed : 28.26 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.47), residues: 288 helix: -0.25 (0.43), residues: 136 sheet: -2.53 (0.90), residues: 34 loop : -2.02 (0.52), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 52 HIS 0.002 0.001 HIS B 68 PHE 0.012 0.001 PHE A 98 TYR 0.009 0.001 TYR B 45 ARG 0.003 0.001 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 0 MET cc_start: 0.5764 (tpp) cc_final: 0.4543 (tpt) REVERT: A 109 LEU cc_start: 0.5904 (OUTLIER) cc_final: 0.5416 (tp) REVERT: B 0 MET cc_start: 0.4520 (tpt) cc_final: 0.4107 (tpt) REVERT: B 98 PHE cc_start: 0.4227 (OUTLIER) cc_final: 0.3514 (t80) outliers start: 16 outliers final: 13 residues processed: 56 average time/residue: 0.1962 time to fit residues: 12.4755 Evaluate side-chains 58 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.0670 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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: 0.3288 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2292 Z= 0.200 Angle : 0.702 13.003 3110 Z= 0.362 Chirality : 0.047 0.173 366 Planarity : 0.005 0.058 406 Dihedral : 6.824 42.565 318 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 28.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 7.83 % Allowed : 30.87 % Favored : 61.30 % 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: -1.57 (0.48), residues: 288 helix: -0.01 (0.45), residues: 124 sheet: -2.28 (0.78), residues: 46 loop : -1.52 (0.54), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 52 HIS 0.002 0.001 HIS A 68 PHE 0.016 0.001 PHE A 152 TYR 0.007 0.001 TYR B 45 ARG 0.009 0.001 ARG B 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 44 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 0 MET cc_start: 0.4620 (tpt) cc_final: 0.4249 (tpt) REVERT: B 98 PHE cc_start: 0.3691 (OUTLIER) cc_final: 0.2706 (t80) outliers start: 18 outliers final: 13 residues processed: 54 average time/residue: 0.1805 time to fit residues: 11.2015 Evaluate side-chains 58 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 0.0470 chunk 26 optimal weight: 0.1980 chunk 27 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.3478 ------------------------------------------------------------------------------- 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: 0.3225 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2292 Z= 0.197 Angle : 0.698 12.704 3110 Z= 0.360 Chirality : 0.047 0.186 366 Planarity : 0.004 0.058 406 Dihedral : 6.900 44.690 318 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 26.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 6.09 % Allowed : 32.17 % Favored : 61.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.48), residues: 288 helix: -0.05 (0.46), residues: 124 sheet: -2.35 (0.77), residues: 46 loop : -1.45 (0.54), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B 52 HIS 0.002 0.000 HIS A 68 PHE 0.010 0.001 PHE A 98 TYR 0.006 0.001 TYR B 45 ARG 0.006 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 0 MET cc_start: 0.5359 (tpp) cc_final: 0.4502 (tpt) REVERT: B 0 MET cc_start: 0.4642 (tpt) cc_final: 0.4358 (tpt) outliers start: 14 outliers final: 9 residues processed: 53 average time/residue: 0.1774 time to fit residues: 10.7319 Evaluate side-chains 57 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 27 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.3375 moved from start: 0.6682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2292 Z= 0.216 Angle : 0.801 13.188 3110 Z= 0.398 Chirality : 0.049 0.216 366 Planarity : 0.005 0.055 406 Dihedral : 6.184 42.362 316 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 33.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.65 % Allowed : 33.04 % Favored : 61.30 % 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: -1.99 (0.47), residues: 288 helix: -0.48 (0.43), residues: 136 sheet: -2.56 (0.74), residues: 46 loop : -1.65 (0.56), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 52 HIS 0.001 0.000 HIS B 68 PHE 0.012 0.001 PHE A 98 TYR 0.006 0.001 TYR B 45 ARG 0.004 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 0 MET cc_start: 0.4671 (tpt) cc_final: 0.4370 (tpt) REVERT: B 115 ARG cc_start: 0.1853 (tpt90) cc_final: 0.1638 (tpt90) outliers start: 13 outliers final: 10 residues processed: 52 average time/residue: 0.1808 time to fit residues: 10.7249 Evaluate side-chains 52 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.0870 chunk 21 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 0.0370 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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: 0.3254 moved from start: 0.6820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2292 Z= 0.201 Angle : 0.820 13.499 3110 Z= 0.403 Chirality : 0.048 0.206 366 Planarity : 0.005 0.057 406 Dihedral : 6.164 42.757 316 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 30.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.35 % Allowed : 34.35 % Favored : 61.30 % 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: -1.72 (0.48), residues: 288 helix: -0.23 (0.44), residues: 124 sheet: -2.61 (0.73), residues: 46 loop : -1.35 (0.56), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 52 HIS 0.002 0.000 HIS A 68 PHE 0.009 0.001 PHE A 98 TYR 0.007 0.001 TYR B 45 ARG 0.008 0.001 ARG A 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 0 MET cc_start: 0.5409 (tpp) cc_final: 0.4535 (tpt) REVERT: B 0 MET cc_start: 0.4827 (tpt) cc_final: 0.4625 (tpt) outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.1702 time to fit residues: 9.6856 Evaluate side-chains 48 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.189719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.157175 restraints weight = 7478.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.158489 restraints weight = 6995.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.159599 restraints weight = 6539.932| |-----------------------------------------------------------------------------| r_work (final): 0.4820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5700 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2292 Z= 0.238 Angle : 0.852 13.309 3110 Z= 0.420 Chirality : 0.050 0.233 366 Planarity : 0.005 0.054 406 Dihedral : 6.435 43.032 316 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 33.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.48 % Allowed : 33.91 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.48), residues: 288 helix: -0.27 (0.45), residues: 124 sheet: -3.19 (0.72), residues: 44 loop : -1.48 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 52 HIS 0.001 0.000 HIS B 157 PHE 0.012 0.001 PHE A 98 TYR 0.003 0.001 TYR B 45 ARG 0.007 0.001 ARG B 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1143.99 seconds wall clock time: 21 minutes 0.69 seconds (1260.69 seconds total)