Starting phenix.real_space_refine on Mon Jan 13 21:21:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uuz_42602/01_2025/8uuz_42602.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uuz_42602/01_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_42602/01_2025/8uuz_42602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uuz_42602/01_2025/8uuz_42602.map" model { file = "/net/cci-nas-00/data/ceres_data/8uuz_42602/01_2025/8uuz_42602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uuz_42602/01_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-5571/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: 2.67, per 1000 atoms: 1.18 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: 0.54 Conformation dependent library (CDL) restraints added in 262.5 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: 0.25 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: 0.51 Time building geometry restraints manager: 0.64 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.120 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.860 ------------------------------------------------------------------------------- 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 : 0.289 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: 0.1830 time to fit residues: 17.7512 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 : 0.236 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.154622 restraints weight = 5482.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.157837 restraints weight = 4580.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.160549 restraints weight = 3904.712| |-----------------------------------------------------------------------------| r_work (final): 0.4865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5785 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 : 0.235 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: 0.9017 (pttp) cc_final: 0.8495 (pttm) REVERT: A 87 GLU cc_start: 0.8104 (tt0) cc_final: 0.7882 (pt0) REVERT: A 109 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8553 (tp) REVERT: B 98 PHE cc_start: 0.6434 (OUTLIER) cc_final: 0.5363 (t80) REVERT: B 109 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8726 (tp) outliers start: 12 outliers final: 5 residues processed: 62 average time/residue: 0.1914 time to fit residues: 13.3647 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 : 0.273 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 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 = 0.5077 r_free = 0.5077 target = 0.186748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.146568 restraints weight = 6570.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.147652 restraints weight = 6307.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.148392 restraints weight = 6044.690| |-----------------------------------------------------------------------------| r_work (final): 0.4712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2292 Z= 0.225 Angle : 0.722 8.644 3110 Z= 0.373 Chirality : 0.048 0.188 366 Planarity : 0.005 0.056 406 Dihedral : 7.885 43.699 322 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 35.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 7.83 % Allowed : 23.91 % 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: -2.02 (0.46), residues: 288 helix: -0.03 (0.43), residues: 132 sheet: -3.17 (0.77), residues: 34 loop : -2.21 (0.49), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 52 HIS 0.001 0.000 HIS B 68 PHE 0.019 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 70 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.233 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 0 MET cc_start: 0.7945 (tpp) cc_final: 0.7576 (tpp) REVERT: A 84 LYS cc_start: 0.8882 (pttp) cc_final: 0.8426 (pttm) REVERT: A 109 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8197 (tp) REVERT: B 0 MET cc_start: 0.8030 (tpp) cc_final: 0.7314 (tpp) REVERT: B 98 PHE cc_start: 0.6158 (OUTLIER) cc_final: 0.5157 (t80) REVERT: B 109 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8406 (tp) REVERT: B 138 ILE cc_start: 0.8422 (pt) cc_final: 0.8049 (mp) outliers start: 18 outliers final: 9 residues processed: 63 average time/residue: 0.1928 time to fit residues: 13.7042 Evaluate side-chains 63 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 84 LYS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 0.0670 chunk 27 optimal weight: 0.0270 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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 = 0.5099 r_free = 0.5099 target = 0.190782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.150637 restraints weight = 6143.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.151437 restraints weight = 5836.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.152757 restraints weight = 5561.315| |-----------------------------------------------------------------------------| r_work (final): 0.4751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5869 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2292 Z= 0.200 Angle : 0.668 7.357 3110 Z= 0.354 Chirality : 0.047 0.174 366 Planarity : 0.005 0.055 406 Dihedral : 7.884 43.034 322 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 29.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 6.96 % Allowed : 23.91 % Favored : 69.13 % 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: -1.85 (0.47), residues: 288 helix: -0.13 (0.43), residues: 134 sheet: -2.76 (0.87), residues: 34 loop : -1.95 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B 52 HIS 0.002 0.001 HIS A 68 PHE 0.012 0.001 PHE A 98 TYR 0.005 0.001 TYR A 45 ARG 0.006 0.001 ARG B 2 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.233 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 9 GLU cc_start: 0.7872 (pm20) cc_final: 0.7539 (pm20) REVERT: B 98 PHE cc_start: 0.5829 (OUTLIER) cc_final: 0.4416 (t80) REVERT: B 109 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8455 (tp) REVERT: B 138 ILE cc_start: 0.8406 (pt) cc_final: 0.8050 (mp) outliers start: 16 outliers final: 10 residues processed: 65 average time/residue: 0.1811 time to fit residues: 13.3314 Evaluate side-chains 62 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 109 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.5037 r_free = 0.5037 target = 0.183259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.139823 restraints weight = 7201.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.140546 restraints weight = 6962.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.140964 restraints weight = 6751.424| |-----------------------------------------------------------------------------| r_work (final): 0.4660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 2292 Z= 0.332 Angle : 0.808 8.523 3110 Z= 0.425 Chirality : 0.052 0.186 366 Planarity : 0.005 0.044 406 Dihedral : 8.281 46.484 320 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 48.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 10.43 % Allowed : 25.65 % 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: -2.62 (0.44), residues: 288 helix: -0.82 (0.42), residues: 134 sheet: -3.81 (0.89), residues: 22 loop : -2.30 (0.47), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.005 TRP A 52 HIS 0.002 0.001 HIS A 157 PHE 0.020 0.002 PHE B 98 TYR 0.006 0.002 TYR B 25 ARG 0.008 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8966 (tp) REVERT: B 2 ARG cc_start: 0.8940 (tpp80) cc_final: 0.8522 (mmm-85) REVERT: B 98 PHE cc_start: 0.6046 (OUTLIER) cc_final: 0.5636 (t80) outliers start: 24 outliers final: 17 residues processed: 61 average time/residue: 0.2048 time to fit residues: 14.0195 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 : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 16 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 109 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 106 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.0670 chunk 13 optimal weight: 0.0770 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.0000 chunk 5 optimal weight: 0.7980 overall best weight: 0.3080 ------------------------------------------------------------------------------- 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 = 0.5114 r_free = 0.5114 target = 0.190653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.152275 restraints weight = 6383.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.153509 restraints weight = 5920.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.155263 restraints weight = 5563.099| |-----------------------------------------------------------------------------| r_work (final): 0.4808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5842 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2292 Z= 0.199 Angle : 0.686 6.976 3110 Z= 0.370 Chirality : 0.047 0.137 366 Planarity : 0.005 0.058 406 Dihedral : 7.644 43.414 320 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.96 % Allowed : 31.74 % Favored : 61.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.46), residues: 288 helix: -0.01 (0.45), residues: 124 sheet: -3.18 (0.98), residues: 22 loop : -1.96 (0.47), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 52 HIS 0.001 0.000 HIS B 68 PHE 0.011 0.001 PHE A 98 TYR 0.007 0.001 TYR B 45 ARG 0.009 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 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: 0.2014 (ttt) cc_final: 0.1806 (ttt) REVERT: B 9 GLU cc_start: 0.8162 (pm20) cc_final: 0.7679 (pm20) REVERT: B 98 PHE cc_start: 0.5553 (OUTLIER) cc_final: 0.4688 (t80) REVERT: B 111 ARG cc_start: 0.6218 (ttt180) cc_final: 0.5513 (mtm-85) REVERT: B 138 ILE cc_start: 0.8449 (pt) cc_final: 0.8132 (mp) outliers start: 16 outliers final: 10 residues processed: 57 average time/residue: 0.1979 time to fit residues: 12.8521 Evaluate side-chains 57 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 126 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.4956 r_free = 0.4956 target = 0.171609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.133302 restraints weight = 6374.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.135412 restraints weight = 5719.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.136750 restraints weight = 5181.760| |-----------------------------------------------------------------------------| r_work (final): 0.4576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 2292 Z= 0.320 Angle : 0.837 11.678 3110 Z= 0.441 Chirality : 0.053 0.163 366 Planarity : 0.006 0.048 406 Dihedral : 7.041 45.649 316 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 46.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 6.96 % Allowed : 31.74 % 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: -2.55 (0.45), residues: 288 helix: -0.48 (0.44), residues: 124 sheet: -4.10 (0.85), residues: 22 loop : -2.44 (0.46), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP A 52 HIS 0.002 0.001 HIS B 68 PHE 0.020 0.002 PHE B 98 TYR 0.007 0.002 TYR B 45 ARG 0.006 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 55 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLU cc_start: 0.8530 (pm20) cc_final: 0.8037 (pm20) REVERT: B 98 PHE cc_start: 0.6171 (OUTLIER) cc_final: 0.5461 (t80) REVERT: B 138 ILE cc_start: 0.8510 (pt) cc_final: 0.8169 (mp) outliers start: 16 outliers final: 13 residues processed: 50 average time/residue: 0.2022 time to fit residues: 11.4575 Evaluate side-chains 51 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 109 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 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 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.5068 r_free = 0.5068 target = 0.185239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.142365 restraints weight = 6629.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.144158 restraints weight = 6132.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.145794 restraints weight = 5706.645| |-----------------------------------------------------------------------------| r_work (final): 0.4756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.6709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2292 Z= 0.226 Angle : 0.744 12.594 3110 Z= 0.389 Chirality : 0.048 0.149 366 Planarity : 0.005 0.054 406 Dihedral : 6.486 44.266 316 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 30.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.78 % Allowed : 33.04 % 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: -2.55 (0.44), residues: 288 helix: -0.48 (0.43), residues: 124 sheet: -3.66 (0.67), residues: 34 loop : -2.30 (0.48), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 52 HIS 0.001 0.001 HIS A 68 PHE 0.013 0.002 PHE B 98 TYR 0.005 0.001 TYR A 45 ARG 0.005 0.001 ARG A 43 *********************** 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 50 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.2411 (ttt) cc_final: 0.2111 (ttt) REVERT: A 111 ARG cc_start: 0.5643 (ttt180) cc_final: 0.5219 (mtm-85) REVERT: B 9 GLU cc_start: 0.8304 (pm20) cc_final: 0.7904 (pm20) REVERT: B 98 PHE cc_start: 0.5691 (OUTLIER) cc_final: 0.4803 (t80) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.1883 time to fit residues: 10.1197 Evaluate side-chains 47 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 108 LEU 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 84 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 0.0470 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.5081 r_free = 0.5081 target = 0.188591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.145813 restraints weight = 6243.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.147119 restraints weight = 5808.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.148740 restraints weight = 5478.791| |-----------------------------------------------------------------------------| r_work (final): 0.4763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.6995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2292 Z= 0.212 Angle : 0.727 12.405 3110 Z= 0.376 Chirality : 0.046 0.143 366 Planarity : 0.005 0.055 406 Dihedral : 6.350 42.569 316 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 28.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.78 % Allowed : 31.30 % 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: -2.31 (0.45), residues: 288 helix: -0.24 (0.44), residues: 124 sheet: -3.80 (0.64), residues: 34 loop : -2.14 (0.49), residues: 130 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 A 98 TYR 0.005 0.001 TYR A 45 ARG 0.004 0.001 ARG A 43 *********************** 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 51 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.2246 (ttt) cc_final: 0.2037 (ttt) REVERT: B 9 GLU cc_start: 0.8272 (pm20) cc_final: 0.7840 (pm20) REVERT: B 98 PHE cc_start: 0.5699 (OUTLIER) cc_final: 0.4748 (t80) REVERT: B 115 ARG cc_start: 0.7255 (tpt170) cc_final: 0.7036 (tpt170) outliers start: 11 outliers final: 8 residues processed: 48 average time/residue: 0.1925 time to fit residues: 10.5896 Evaluate side-chains 48 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 108 LEU 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 84 LYS Chi-restraints excluded: chain B residue 98 PHE 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: 0.9990 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 0.0000 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 = 0.5109 r_free = 0.5109 target = 0.191956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.153757 restraints weight = 6825.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.156051 restraints weight = 6200.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.157850 restraints weight = 5612.262| |-----------------------------------------------------------------------------| r_work (final): 0.4732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.7345 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= 0.218 Angle : 0.770 12.836 3110 Z= 0.397 Chirality : 0.048 0.155 366 Planarity : 0.005 0.054 406 Dihedral : 6.339 42.229 316 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 28.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.91 % Allowed : 33.48 % 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: -2.35 (0.46), residues: 288 helix: -0.27 (0.45), residues: 124 sheet: -4.00 (0.63), residues: 34 loop : -2.11 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP B 52 HIS 0.001 0.000 HIS A 68 PHE 0.013 0.002 PHE A 98 TYR 0.007 0.001 TYR B 140 ARG 0.005 0.001 ARG A 115 ********************** 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 47 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.2266 (ttt) cc_final: 0.2045 (ttt) REVERT: B 9 GLU cc_start: 0.8432 (pm20) cc_final: 0.7903 (pm20) REVERT: B 98 PHE cc_start: 0.5781 (OUTLIER) cc_final: 0.4965 (t80) REVERT: B 115 ARG cc_start: 0.7484 (tpt170) cc_final: 0.7219 (tpt170) outliers start: 9 outliers final: 8 residues processed: 45 average time/residue: 0.1973 time to fit residues: 10.1143 Evaluate side-chains 45 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 108 LEU 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 84 LYS Chi-restraints excluded: chain B residue 98 PHE 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: 0.9980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.5066 r_free = 0.5066 target = 0.182999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.148551 restraints weight = 6828.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.150668 restraints weight = 6103.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.152505 restraints weight = 5536.457| |-----------------------------------------------------------------------------| r_work (final): 0.4758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.7703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2292 Z= 0.222 Angle : 0.761 12.902 3110 Z= 0.394 Chirality : 0.047 0.145 366 Planarity : 0.005 0.055 406 Dihedral : 6.219 39.664 316 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 27.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.78 % Allowed : 32.17 % Favored : 63.04 % 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: -2.39 (0.46), residues: 288 helix: -0.24 (0.45), residues: 124 sheet: -4.21 (0.59), residues: 34 loop : -2.12 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 52 HIS 0.001 0.000 HIS A 68 PHE 0.013 0.001 PHE A 98 TYR 0.011 0.002 TYR B 140 ARG 0.003 0.001 ARG A 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1417.81 seconds wall clock time: 25 minutes 55.40 seconds (1555.40 seconds total)