Starting phenix.real_space_refine on Wed Mar 5 23:46:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uuz_42602/03_2025/8uuz_42602.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uuz_42602/03_2025/8uuz_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/cci-nas-00/data/ceres_data/8uuz_42602/03_2025/8uuz_42602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uuz_42602/03_2025/8uuz_42602.map" model { file = "/net/cci-nas-00/data/ceres_data/8uuz_42602/03_2025/8uuz_42602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uuz_42602/03_2025/8uuz_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. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 2.78, per 1000 atoms: 1.23 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 - 3.00 Amino acid : True - 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: 0.60 Conformation dependent library (CDL) restraints added in 293.3 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: 0.22 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: 0.71 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: 0.00 - 1.44: 2982 1.44 - 2.88: 91 2.88 - 4.32: 23 4.32 - 5.75: 10 5.75 - 7.19: 4 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: 0.01 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: 13.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.690 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- 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 to be fit. 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: 0.1745 time to fit residues: 16.9101 Evaluate side-chains 62 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5152 r_free = 0.5152 target = 0.189977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.154520 restraints weight = 5482.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.157800 restraints weight = 4583.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.160412 restraints weight = 3912.991| |-----------------------------------------------------------------------------| r_work (final): 0.4957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 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 to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8714 (pttp) cc_final: 0.8236 (pttm) REVERT: A 109 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8149 (tp) REVERT: B 98 PHE cc_start: 0.6269 (OUTLIER) cc_final: 0.5181 (t80) REVERT: B 109 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8435 (tp) outliers start: 12 outliers final: 5 residues processed: 62 average time/residue: 0.2034 time to fit residues: 14.2129 Evaluate side-chains 59 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.5544 r_free = 0.5544 target = 0.244412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5522 r_free = 0.5522 target = 0.219253 restraints weight = 11267.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.5527 r_free = 0.5527 target = 0.221244 restraints weight = 9222.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5571 r_free = 0.5571 target = 0.223458 restraints weight = 7927.126| |-----------------------------------------------------------------------------| r_work (final): 0.4878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 0.4218 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= 0.206 Angle : 0.704 8.442 3110 Z= 0.367 Chirality : 0.047 0.186 366 Planarity : 0.005 0.057 406 Dihedral : 7.770 43.019 322 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 32.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 7.39 % Allowed : 24.35 % 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: -1.90 (0.46), residues: 288 helix: -0.01 (0.43), residues: 134 sheet: -3.15 (0.75), residues: 34 loop : -2.08 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 52 HIS 0.002 0.000 HIS A 68 PHE 0.020 0.002 PHE A 152 TYR 0.007 0.001 TYR B 140 ARG 0.005 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 72 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.742 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: 0.7853 (tpp) cc_final: 0.7478 (tpp) REVERT: A 109 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8184 (tp) REVERT: A 115 ARG cc_start: 0.6874 (tpt90) cc_final: 0.5879 (tpt90) REVERT: B 0 MET cc_start: 0.7977 (tpp) cc_final: 0.7221 (tpp) REVERT: B 98 PHE cc_start: 0.6081 (OUTLIER) cc_final: 0.4992 (t80) REVERT: B 109 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8257 (tp) REVERT: B 115 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6098 (tpt90) REVERT: B 136 GLU cc_start: 0.8327 (mp0) cc_final: 0.8001 (pp20) REVERT: B 138 ILE cc_start: 0.8343 (pt) cc_final: 0.8014 (mp) outliers start: 17 outliers final: 7 residues processed: 64 average time/residue: 0.2439 time to fit residues: 17.8660 Evaluate side-chains 65 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET 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 98 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.5082 r_free = 0.5082 target = 0.184138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.148840 restraints weight = 6421.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.150283 restraints weight = 5953.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.151268 restraints weight = 5554.927| |-----------------------------------------------------------------------------| r_work (final): 0.4679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.4646 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= 0.217 Angle : 0.682 7.630 3110 Z= 0.357 Chirality : 0.048 0.181 366 Planarity : 0.005 0.052 406 Dihedral : 7.997 43.837 322 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 34.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 10.00 % Allowed : 21.30 % 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: -2.00 (0.46), residues: 288 helix: -0.26 (0.42), residues: 134 sheet: -2.78 (0.88), residues: 34 loop : -2.03 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP B 52 HIS 0.002 0.001 HIS B 68 PHE 0.013 0.002 PHE B 98 TYR 0.004 0.001 TYR B 45 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 78 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.229 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 9 GLU cc_start: 0.8024 (pm20) cc_final: 0.7736 (pm20) REVERT: A 78 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7201 (mtt) REVERT: A 109 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8322 (tp) REVERT: A 111 ARG cc_start: 0.5659 (ttt180) cc_final: 0.5185 (mtm-85) REVERT: B 98 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5305 (t80) REVERT: B 109 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8626 (tp) REVERT: B 115 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7428 (tpt170) REVERT: B 138 ILE cc_start: 0.8417 (pt) cc_final: 0.8055 (mp) outliers start: 23 outliers final: 13 residues processed: 67 average time/residue: 0.1879 time to fit residues: 14.1702 Evaluate side-chains 67 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 92 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 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 106 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 115 ARG 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 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.5503 r_free = 0.5503 target = 0.237339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5475 r_free = 0.5475 target = 0.210628 restraints weight = 11628.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5508 r_free = 0.5508 target = 0.213277 restraints weight = 9249.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5524 r_free = 0.5524 target = 0.215289 restraints weight = 7707.519| |-----------------------------------------------------------------------------| r_work (final): 0.4772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.5054 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= 0.244 Angle : 0.706 7.759 3110 Z= 0.369 Chirality : 0.047 0.170 366 Planarity : 0.005 0.049 406 Dihedral : 8.145 44.938 322 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 37.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 10.43 % Allowed : 24.78 % 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: -2.11 (0.46), residues: 288 helix: -0.39 (0.42), residues: 136 sheet: -2.70 (0.92), residues: 34 loop : -2.10 (0.50), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP A 52 HIS 0.001 0.000 HIS B 68 PHE 0.014 0.002 PHE B 98 TYR 0.005 0.001 TYR B 25 ARG 0.005 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 73 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 49 time to evaluate : 0.253 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: 0.7830 (tpt) cc_final: 0.7524 (tpt) REVERT: B 0 MET cc_start: 0.7974 (tpp) cc_final: 0.7719 (tpp) REVERT: B 98 PHE cc_start: 0.6273 (OUTLIER) cc_final: 0.5321 (t80) REVERT: B 109 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8496 (tp) REVERT: B 115 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7205 (tpt170) REVERT: B 138 ILE cc_start: 0.8412 (pt) cc_final: 0.8067 (mp) outliers start: 24 outliers final: 16 residues processed: 63 average time/residue: 0.2146 time to fit residues: 15.1308 Evaluate side-chains 64 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 115 ARG 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 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 109 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 115 ARG 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 15 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.5071 r_free = 0.5071 target = 0.186088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.144454 restraints weight = 6099.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.145909 restraints weight = 5702.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.147247 restraints weight = 5366.166| |-----------------------------------------------------------------------------| r_work (final): 0.4820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 0.5531 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= 0.233 Angle : 0.747 8.823 3110 Z= 0.395 Chirality : 0.048 0.161 366 Planarity : 0.005 0.055 406 Dihedral : 7.592 44.746 320 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 33.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 10.43 % Allowed : 27.39 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.46), residues: 288 helix: -0.41 (0.43), residues: 136 sheet: -2.98 (0.87), residues: 34 loop : -2.11 (0.51), residues: 118 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 0.013 0.002 PHE B 98 TYR 0.004 0.001 TYR B 45 ARG 0.005 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 71 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 0.271 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 0 MET cc_start: 0.7892 (tpt) cc_final: 0.7567 (tpt) REVERT: A 98 PHE cc_start: 0.6059 (OUTLIER) cc_final: 0.5391 (t80) REVERT: B 2 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7770 (mmm-85) REVERT: B 98 PHE cc_start: 0.5963 (OUTLIER) cc_final: 0.4924 (t80) REVERT: B 109 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8122 (tp) REVERT: B 138 ILE cc_start: 0.8422 (pt) cc_final: 0.8096 (mp) outliers start: 24 outliers final: 15 residues processed: 60 average time/residue: 0.2037 time to fit residues: 13.6919 Evaluate side-chains 62 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE 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 108 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 16 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 23 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.197833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.147661 restraints weight = 7040.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.147736 restraints weight = 7003.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.147736 restraints weight = 6989.344| |-----------------------------------------------------------------------------| r_work (final): 0.4714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2292 Z= 0.239 Angle : 0.740 8.458 3110 Z= 0.392 Chirality : 0.049 0.156 366 Planarity : 0.005 0.056 406 Dihedral : 7.087 44.020 318 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 32.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 9.13 % Allowed : 28.26 % 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: -1.93 (0.47), residues: 288 helix: 0.00 (0.45), residues: 124 sheet: -3.19 (0.76), residues: 44 loop : -1.79 (0.51), residues: 120 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 0.014 0.001 PHE B 98 TYR 0.007 0.001 TYR B 45 ARG 0.004 0.001 ARG A 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 64 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.5791 (OUTLIER) cc_final: 0.5252 (t80) REVERT: B 9 GLU cc_start: 0.8472 (pm20) cc_final: 0.7923 (pm20) REVERT: B 98 PHE cc_start: 0.5830 (OUTLIER) cc_final: 0.5223 (t80) REVERT: B 109 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8742 (tp) REVERT: B 115 ARG cc_start: 0.7978 (tpt170) cc_final: 0.7733 (tpt170) outliers start: 21 outliers final: 15 residues processed: 56 average time/residue: 0.2374 time to fit residues: 15.0999 Evaluate side-chains 58 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE 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 108 LEU Chi-restraints excluded: chain A residue 115 ARG 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 78 MET 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 109 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 21 optimal weight: 0.0770 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.5070 r_free = 0.5070 target = 0.186584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.150925 restraints weight = 7614.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.152240 restraints weight = 7264.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.153098 restraints weight = 6874.129| |-----------------------------------------------------------------------------| r_work (final): 0.4756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2292 Z= 0.217 Angle : 0.723 7.252 3110 Z= 0.386 Chirality : 0.048 0.147 366 Planarity : 0.005 0.057 406 Dihedral : 7.057 43.715 318 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 29.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 8.26 % Allowed : 30.43 % 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: -2.47 (0.47), residues: 288 helix: -0.35 (0.43), residues: 136 sheet: -3.65 (0.58), residues: 52 loop : -2.10 (0.56), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 52 HIS 0.001 0.000 HIS B 68 PHE 0.012 0.001 PHE A 98 TYR 0.004 0.001 TYR B 45 ARG 0.003 0.001 ARG B 2 *********************** 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 60 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.5876 (OUTLIER) cc_final: 0.5316 (t80) REVERT: A 115 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.4537 (ptt180) REVERT: B 0 MET cc_start: 0.6551 (tpt) cc_final: 0.6244 (tpt) REVERT: B 9 GLU cc_start: 0.8196 (pm20) cc_final: 0.7585 (pm20) REVERT: B 78 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7570 (mtt) REVERT: B 91 LEU cc_start: 0.9384 (mt) cc_final: 0.9039 (mt) REVERT: B 98 PHE cc_start: 0.5396 (OUTLIER) cc_final: 0.4287 (t80) REVERT: B 109 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8063 (tp) REVERT: B 115 ARG cc_start: 0.6723 (tpt170) cc_final: 0.6370 (tpt90) outliers start: 19 outliers final: 12 residues processed: 53 average time/residue: 0.1946 time to fit residues: 11.7097 Evaluate side-chains 57 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 115 ARG 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 68 HIS Chi-restraints excluded: chain B residue 78 MET 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 109 LEU Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.0030 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 7 optimal weight: 0.3980 chunk 27 optimal weight: 0.0970 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- 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 = 0.5111 r_free = 0.5111 target = 0.193162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.162254 restraints weight = 7903.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.163310 restraints weight = 7326.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.164707 restraints weight = 6811.855| |-----------------------------------------------------------------------------| r_work (final): 0.4823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.6933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2292 Z= 0.217 Angle : 0.724 8.105 3110 Z= 0.387 Chirality : 0.047 0.142 366 Planarity : 0.005 0.059 406 Dihedral : 6.913 50.078 318 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 26.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 6.52 % Allowed : 31.74 % 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: -2.31 (0.48), residues: 288 helix: -0.29 (0.43), residues: 136 sheet: -3.43 (0.55), residues: 64 loop : -1.63 (0.63), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 52 HIS 0.001 0.000 HIS A 44 PHE 0.010 0.001 PHE A 98 TYR 0.008 0.002 TYR B 25 ARG 0.005 0.001 ARG A 2 *********************** 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 to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.4797 (ptt180) REVERT: B 9 GLU cc_start: 0.8290 (pm20) cc_final: 0.7706 (pm20) REVERT: B 78 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7377 (mtt) REVERT: B 91 LEU cc_start: 0.9345 (mt) cc_final: 0.9008 (mt) outliers start: 15 outliers final: 11 residues processed: 55 average time/residue: 0.1849 time to fit residues: 11.5953 Evaluate side-chains 58 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 78 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 0.0370 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.194454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.157298 restraints weight = 7751.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.159275 restraints weight = 7134.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.160478 restraints weight = 6589.851| |-----------------------------------------------------------------------------| r_work (final): 0.4761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5915 moved from start: 0.7204 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= 0.206 Angle : 0.811 12.937 3110 Z= 0.407 Chirality : 0.048 0.180 366 Planarity : 0.005 0.057 406 Dihedral : 6.080 41.187 316 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 29.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.09 % Allowed : 31.74 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.49), residues: 288 helix: -0.04 (0.47), residues: 124 sheet: -3.50 (0.54), residues: 64 loop : -1.39 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 52 HIS 0.001 0.000 HIS A 68 PHE 0.013 0.001 PHE A 98 TYR 0.008 0.002 TYR B 25 ARG 0.007 0.001 ARG A 2 ********************** 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 59 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.1972 (ttt) cc_final: 0.1712 (mtp) REVERT: A 87 GLU cc_start: 0.7385 (pt0) cc_final: 0.6768 (pt0) REVERT: A 98 PHE cc_start: 0.5730 (OUTLIER) cc_final: 0.5249 (t80) REVERT: A 115 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.4848 (ptt180) REVERT: B 9 GLU cc_start: 0.8348 (pm20) cc_final: 0.7679 (pm20) REVERT: B 78 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7604 (mtt) REVERT: B 91 LEU cc_start: 0.9436 (mt) cc_final: 0.9067 (mt) REVERT: B 115 ARG cc_start: 0.7183 (tpt170) cc_final: 0.6976 (tpt90) outliers start: 14 outliers final: 9 residues processed: 53 average time/residue: 0.2524 time to fit residues: 15.3593 Evaluate side-chains 56 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 0.0370 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5095 r_free = 0.5095 target = 0.192735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.161960 restraints weight = 7787.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.163730 restraints weight = 7056.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.165385 restraints weight = 6462.947| |-----------------------------------------------------------------------------| r_work (final): 0.4779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.7457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2292 Z= 0.209 Angle : 0.853 13.475 3110 Z= 0.421 Chirality : 0.048 0.183 366 Planarity : 0.005 0.057 406 Dihedral : 6.102 41.675 316 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 31.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.78 % Allowed : 33.91 % 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: -2.29 (0.49), residues: 288 helix: -0.17 (0.46), residues: 124 sheet: -3.60 (0.53), residues: 64 loop : -1.51 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 52 HIS 0.001 0.000 HIS A 68 PHE 0.011 0.001 PHE A 98 TYR 0.010 0.002 TYR B 140 ARG 0.007 0.001 ARG A 2 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2070.34 seconds wall clock time: 37 minutes 48.59 seconds (2268.59 seconds total)