Starting phenix.real_space_refine on Mon Jun 24 19:32:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuz_42602/06_2024/8uuz_42602.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuz_42602/06_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_42602/06_2024/8uuz_42602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuz_42602/06_2024/8uuz_42602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuz_42602/06_2024/8uuz_42602.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuz_42602/06_2024/8uuz_42602.pdb" } 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-5370/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: 2.89, per 1000 atoms: 1.28 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: 0.86 Conformation dependent library (CDL) restraints added in 413.8 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: 0.21 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: 0.48 Time building geometry restraints manager: 0.96 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 2.520 nonbonded pdb=" O ILE B 88 " pdb=" NZ LYS B 92 " model vdw 2.214 2.520 nonbonded pdb=" OD2 ASP B 28 " pdb=" OH TYR B 45 " model vdw 2.228 2.440 nonbonded pdb=" ND2 ASN A 13 " pdb=" O SER A 30 " model vdw 2.258 2.520 nonbonded pdb=" OD2 ASP A 28 " pdb=" OH TYR A 45 " model vdw 2.265 2.440 ... (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 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: 1.910 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: 8.870 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.520 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- 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 : 0.262 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: 0.1866 time to fit residues: 18.0466 Evaluate side-chains 62 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 0.0030 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN B 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3419 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2292 Z= 0.202 Angle : 0.754 9.649 3110 Z= 0.375 Chirality : 0.048 0.237 366 Planarity : 0.005 0.049 406 Dihedral : 8.780 44.186 330 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 34.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 6.52 % Allowed : 26.96 % Favored : 66.52 % 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: 0.46 (0.45), residues: 120 sheet: -3.24 (0.77), residues: 34 loop : -1.83 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.004 TRP B 52 HIS 0.002 0.001 HIS A 68 PHE 0.019 0.002 PHE B 152 TYR 0.007 0.001 TYR B 140 ARG 0.001 0.000 ARG A 160 *********************** 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 72 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.266 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 78 MET cc_start: 0.5921 (tpt) cc_final: 0.5443 (tpp) REVERT: A 109 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5385 (tp) REVERT: B 109 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5461 (tp) outliers start: 15 outliers final: 7 residues processed: 67 average time/residue: 0.1933 time to fit residues: 14.5811 Evaluate side-chains 61 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 THR Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 85 ASP 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: 0.9990 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 14 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3439 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2292 Z= 0.207 Angle : 0.678 8.823 3110 Z= 0.351 Chirality : 0.047 0.169 366 Planarity : 0.005 0.055 406 Dihedral : 7.737 42.431 322 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 37.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 8.26 % Allowed : 24.78 % 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: -1.65 (0.48), residues: 288 helix: 0.12 (0.44), residues: 134 sheet: -2.71 (0.88), residues: 34 loop : -1.96 (0.52), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 52 HIS 0.002 0.000 HIS B 68 PHE 0.014 0.002 PHE B 98 TYR 0.006 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 73 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 0.258 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 86 THR cc_start: 0.5919 (m) cc_final: 0.5566 (m) REVERT: A 109 LEU cc_start: 0.5679 (OUTLIER) cc_final: 0.5194 (tp) REVERT: B 98 PHE cc_start: 0.4479 (OUTLIER) cc_final: 0.3771 (t80) REVERT: B 109 LEU cc_start: 0.5759 (OUTLIER) cc_final: 0.5306 (tp) outliers start: 19 outliers final: 12 residues processed: 64 average time/residue: 0.1877 time to fit residues: 13.6668 Evaluate side-chains 65 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 50 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 15 THR Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 85 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3490 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2292 Z= 0.213 Angle : 0.664 7.796 3110 Z= 0.349 Chirality : 0.046 0.167 366 Planarity : 0.005 0.052 406 Dihedral : 7.899 43.091 322 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 41.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 9.57 % Allowed : 26.52 % Favored : 63.91 % 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: -1.69 (0.48), residues: 288 helix: 0.01 (0.44), residues: 134 sheet: -2.60 (0.90), residues: 34 loop : -1.91 (0.52), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 52 HIS 0.002 0.000 HIS B 68 PHE 0.020 0.002 PHE A 152 TYR 0.004 0.001 TYR A 140 ARG 0.007 0.001 ARG A 115 *********************** 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 76 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 54 time to evaluate : 0.266 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: B 98 PHE cc_start: 0.4752 (OUTLIER) cc_final: 0.3843 (t80) REVERT: B 109 LEU cc_start: 0.5772 (OUTLIER) cc_final: 0.5452 (tp) outliers start: 22 outliers final: 16 residues processed: 64 average time/residue: 0.1909 time to fit residues: 13.8508 Evaluate side-chains 67 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 49 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 56 ASP 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 56 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 108 LEU 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: 1.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.0020 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3699 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2292 Z= 0.268 Angle : 0.719 8.410 3110 Z= 0.381 Chirality : 0.048 0.147 366 Planarity : 0.005 0.052 406 Dihedral : 8.172 45.062 322 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 49.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 10.87 % Allowed : 31.30 % Favored : 57.83 % 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: -1.94 (0.48), residues: 288 helix: -0.18 (0.45), residues: 136 sheet: -2.72 (0.89), residues: 34 loop : -2.09 (0.51), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP A 52 HIS 0.001 0.000 HIS A 157 PHE 0.017 0.002 PHE B 98 TYR 0.004 0.001 TYR B 140 ARG 0.006 0.001 ARG B 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 75 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 50 time to evaluate : 0.272 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 109 LEU cc_start: 0.6000 (OUTLIER) cc_final: 0.5231 (tp) REVERT: B 98 PHE cc_start: 0.5074 (OUTLIER) cc_final: 0.4700 (t80) REVERT: B 109 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5567 (tp) outliers start: 25 outliers final: 20 residues processed: 63 average time/residue: 0.2108 time to fit residues: 14.8689 Evaluate side-chains 70 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 47 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 108 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.4980 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.0870 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 0.0370 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN B 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3407 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2292 Z= 0.201 Angle : 0.668 6.638 3110 Z= 0.355 Chirality : 0.046 0.141 366 Planarity : 0.005 0.057 406 Dihedral : 7.698 43.315 322 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 34.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 10.00 % Allowed : 32.17 % Favored : 57.83 % 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: -1.84 (0.47), residues: 288 helix: -0.23 (0.43), residues: 136 sheet: -2.68 (0.87), residues: 34 loop : -1.85 (0.53), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 52 HIS 0.001 0.000 HIS A 68 PHE 0.020 0.002 PHE A 152 TYR 0.004 0.001 TYR B 140 ARG 0.007 0.001 ARG B 115 *********************** 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 72 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 49 time to evaluate : 0.279 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 109 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.5226 (tp) REVERT: B 98 PHE cc_start: 0.4170 (OUTLIER) cc_final: 0.3527 (t80) REVERT: B 109 LEU cc_start: 0.5725 (OUTLIER) cc_final: 0.5195 (tp) outliers start: 23 outliers final: 18 residues processed: 62 average time/residue: 0.2140 time to fit residues: 14.8562 Evaluate side-chains 68 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 47 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 107 ILE 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 4 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 85 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 109 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: 3.9990 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 13 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.3467 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2292 Z= 0.211 Angle : 0.714 9.377 3110 Z= 0.374 Chirality : 0.048 0.158 366 Planarity : 0.004 0.055 406 Dihedral : 7.739 42.328 322 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 39.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 10.43 % Allowed : 32.17 % Favored : 57.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.49), residues: 288 helix: -0.09 (0.44), residues: 134 sheet: -2.75 (0.82), residues: 44 loop : -1.68 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 52 HIS 0.001 0.000 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 A 111 *********************** 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 74 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 50 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 0 MET cc_start: 0.4655 (tpt) cc_final: 0.4305 (tpt) REVERT: A 98 PHE cc_start: 0.4619 (OUTLIER) cc_final: 0.3939 (t80) REVERT: B 76 MET cc_start: 0.2485 (ttt) cc_final: 0.1802 (ttt) REVERT: B 98 PHE cc_start: 0.4559 (OUTLIER) cc_final: 0.3757 (t80) outliers start: 24 outliers final: 17 residues processed: 63 average time/residue: 0.1935 time to fit residues: 13.6714 Evaluate side-chains 69 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 ILE 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 85 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: 0.9980 chunk 22 optimal weight: 0.0980 chunk 26 optimal weight: 0.0270 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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: 0.3398 moved from start: 0.5921 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= 0.189 Angle : 0.781 10.513 3110 Z= 0.409 Chirality : 0.047 0.135 366 Planarity : 0.005 0.056 406 Dihedral : 6.447 41.637 318 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 34.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 7.39 % Allowed : 35.22 % Favored : 57.39 % 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: -1.61 (0.48), residues: 288 helix: 0.07 (0.45), residues: 122 sheet: -2.94 (0.79), residues: 44 loop : -1.39 (0.52), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 52 HIS 0.002 0.000 HIS A 68 PHE 0.015 0.002 PHE A 152 TYR 0.005 0.001 TYR B 140 ARG 0.012 0.001 ARG A 111 *********************** 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 64 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 0.247 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: 0.4767 (tpt) cc_final: 0.4492 (tpt) REVERT: B 0 MET cc_start: 0.5438 (tpp) cc_final: 0.4288 (tpt) REVERT: B 76 MET cc_start: 0.2136 (ttt) cc_final: 0.1256 (ttt) REVERT: B 86 THR cc_start: 0.6082 (m) cc_final: 0.5585 (m) REVERT: B 98 PHE cc_start: 0.4180 (OUTLIER) cc_final: 0.3425 (t80) outliers start: 17 outliers final: 13 residues processed: 58 average time/residue: 0.2065 time to fit residues: 13.4873 Evaluate side-chains 59 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 98 PHE 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: 0.6980 chunk 17 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.3497 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2292 Z= 0.180 Angle : 0.761 12.750 3110 Z= 0.392 Chirality : 0.049 0.167 366 Planarity : 0.005 0.053 406 Dihedral : 6.415 40.732 318 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 36.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 6.96 % Allowed : 37.83 % Favored : 55.22 % 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: -1.80 (0.48), residues: 288 helix: -0.10 (0.46), residues: 124 sheet: -3.03 (0.79), residues: 44 loop : -1.49 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 52 HIS 0.001 0.000 HIS B 68 PHE 0.014 0.001 PHE B 98 TYR 0.005 0.001 TYR B 140 ARG 0.011 0.001 ARG A 111 *********************** 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 61 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 0 MET cc_start: 0.4852 (tpt) cc_final: 0.4618 (tpt) REVERT: A 98 PHE cc_start: 0.4507 (OUTLIER) cc_final: 0.4080 (t80) REVERT: A 108 LEU cc_start: 0.6175 (mm) cc_final: 0.5612 (mm) REVERT: B 0 MET cc_start: 0.5621 (tpp) cc_final: 0.4529 (tpt) REVERT: B 86 THR cc_start: 0.6008 (m) cc_final: 0.5513 (m) REVERT: B 98 PHE cc_start: 0.4525 (OUTLIER) cc_final: 0.3725 (t80) outliers start: 16 outliers final: 13 residues processed: 56 average time/residue: 0.1847 time to fit residues: 11.7982 Evaluate side-chains 59 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 98 PHE 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: 2.9990 chunk 21 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.0270 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- 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: 0.3449 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2292 Z= 0.187 Angle : 0.828 12.010 3110 Z= 0.418 Chirality : 0.050 0.211 366 Planarity : 0.005 0.057 406 Dihedral : 6.447 40.937 318 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 37.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 7.39 % Allowed : 36.52 % Favored : 56.09 % 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 (0.48), residues: 288 helix: -0.30 (0.46), residues: 124 sheet: -2.80 (0.76), residues: 46 loop : -1.53 (0.54), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 52 HIS 0.001 0.000 HIS A 68 PHE 0.013 0.001 PHE B 98 TYR 0.005 0.001 TYR B 140 ARG 0.012 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 64 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.4457 (OUTLIER) cc_final: 0.3752 (t80) REVERT: B 0 MET cc_start: 0.5689 (tpp) cc_final: 0.4576 (tpt) REVERT: B 86 THR cc_start: 0.6006 (m) cc_final: 0.5507 (m) REVERT: B 98 PHE cc_start: 0.4039 (OUTLIER) cc_final: 0.3334 (t80) outliers start: 17 outliers final: 15 residues processed: 57 average time/residue: 0.1806 time to fit residues: 11.7327 Evaluate side-chains 64 residues out of total 260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 85 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.5040 r_free = 0.5040 target = 0.189811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.151886 restraints weight = 6552.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.152850 restraints weight = 6249.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.153403 restraints weight = 5990.800| |-----------------------------------------------------------------------------| r_work (final): 0.4690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.6595 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= 0.195 Angle : 0.834 11.983 3110 Z= 0.421 Chirality : 0.049 0.186 366 Planarity : 0.005 0.063 406 Dihedral : 6.455 41.162 318 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 38.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 6.52 % Allowed : 36.96 % Favored : 56.52 % 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 (0.48), residues: 288 helix: -0.40 (0.46), residues: 124 sheet: -2.93 (0.73), residues: 46 loop : -1.46 (0.56), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A 52 HIS 0.001 0.000 HIS A 68 PHE 0.013 0.001 PHE B 98 TYR 0.004 0.001 TYR B 25 ARG 0.011 0.001 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1238.70 seconds wall clock time: 22 minutes 52.24 seconds (1372.24 seconds total)