Starting phenix.real_space_refine on Fri Dec 27 12:51:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eir_28162/12_2024/8eir_28162.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eir_28162/12_2024/8eir_28162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eir_28162/12_2024/8eir_28162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eir_28162/12_2024/8eir_28162.map" model { file = "/net/cci-nas-00/data/ceres_data/8eir_28162/12_2024/8eir_28162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eir_28162/12_2024/8eir_28162.cif" } resolution = 2.49 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= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 3080 2.51 5 N 834 2.21 5 O 914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2366 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain: "B" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2366 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 69 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 69 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Time building chain proxies: 3.76, per 1000 atoms: 0.77 Number of scatterers: 4870 At special positions: 0 Unit cell: (88.065, 70.11, 76.95, 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 42 16.00 O 914 8.00 N 834 7.00 C 3080 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: 1.13 Conformation dependent library (CDL) restraints added in 545.9 milliseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1156 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 28.8% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.542A pdb=" N ARG A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.808A pdb=" N LYS A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 41 through 44 Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.579A pdb=" N ARG B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 Processing helix chain 'B' and resid 200 through 214 Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.783A pdb=" N LYS B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 292 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 75 removed outlier: 4.520A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ASN A 28 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 removed outlier: 5.550A pdb=" N HIS A 163 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR A 175 " --> pdb=" O HIS A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 129 removed outlier: 6.823A pdb=" N ALA A 116 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 125 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 114 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLN A 127 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE A 112 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 11.351A pdb=" N THR A 111 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE A 152 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 148 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY A 149 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 75 removed outlier: 4.483A pdb=" N VAL B 68 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASN B 28 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 103 removed outlier: 6.982A pdb=" N ALA B 173 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 129 removed outlier: 6.831A pdb=" N ALA B 116 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 125 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 114 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN B 127 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE B 112 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N THR B 111 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE B 152 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 148 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY B 149 " --> pdb=" O CYS B 160 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1570 1.34 - 1.45: 705 1.45 - 1.57: 2637 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 4974 Sorted by residual: bond pdb=" CA ASN A 277 " pdb=" CB ASN A 277 " ideal model delta sigma weight residual 1.529 1.558 -0.029 1.62e-02 3.81e+03 3.18e+00 bond pdb=" CB ASN A 277 " pdb=" CG ASN A 277 " ideal model delta sigma weight residual 1.516 1.560 -0.044 2.50e-02 1.60e+03 3.09e+00 bond pdb=" C LEU A 167 " pdb=" N PRO A 168 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.68e+00 bond pdb=" CA ASN A 277 " pdb=" C ASN A 277 " ideal model delta sigma weight residual 1.526 1.541 -0.015 1.29e-02 6.01e+03 1.38e+00 bond pdb=" C LEU B 167 " pdb=" N PRO B 168 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.27e+00 ... (remaining 4969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 6567 1.99 - 3.98: 158 3.98 - 5.98: 25 5.98 - 7.97: 4 7.97 - 9.96: 4 Bond angle restraints: 6758 Sorted by residual: angle pdb=" CA ASN A 277 " pdb=" CB ASN A 277 " pdb=" CG ASN A 277 " ideal model delta sigma weight residual 112.60 116.85 -4.25 1.00e+00 1.00e+00 1.81e+01 angle pdb=" CA MET B 49 " pdb=" CB MET B 49 " pdb=" CG MET B 49 " ideal model delta sigma weight residual 114.10 121.23 -7.13 2.00e+00 2.50e-01 1.27e+01 angle pdb=" C ASN A 277 " pdb=" CA ASN A 277 " pdb=" CB ASN A 277 " ideal model delta sigma weight residual 111.80 116.89 -5.09 1.46e+00 4.69e-01 1.21e+01 angle pdb=" CA ARG B 217 " pdb=" CB ARG B 217 " pdb=" CG ARG B 217 " ideal model delta sigma weight residual 114.10 120.82 -6.72 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CB MET A 17 " pdb=" CG MET A 17 " pdb=" SD MET A 17 " ideal model delta sigma weight residual 112.70 121.99 -9.29 3.00e+00 1.11e-01 9.60e+00 ... (remaining 6753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 2554 16.91 - 33.82: 256 33.82 - 50.73: 86 50.73 - 67.64: 29 67.64 - 84.55: 3 Dihedral angle restraints: 2928 sinusoidal: 1122 harmonic: 1806 Sorted by residual: dihedral pdb=" CA ASP A 245 " pdb=" CB ASP A 245 " pdb=" CG ASP A 245 " pdb=" OD1 ASP A 245 " ideal model delta sinusoidal sigma weight residual -30.00 -86.78 56.78 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA THR A 175 " pdb=" C THR A 175 " pdb=" N ASP A 176 " pdb=" CA ASP A 176 " ideal model delta harmonic sigma weight residual 180.00 163.89 16.11 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA PHE B 181 " pdb=" C PHE B 181 " pdb=" N TYR B 182 " pdb=" CA TYR B 182 " ideal model delta harmonic sigma weight residual 180.00 163.96 16.04 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 447 0.039 - 0.077: 226 0.077 - 0.116: 81 0.116 - 0.154: 7 0.154 - 0.192: 5 Chirality restraints: 766 Sorted by residual: chirality pdb=" CA HIS A 41 " pdb=" N HIS A 41 " pdb=" C HIS A 41 " pdb=" CB HIS A 41 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA HIS B 41 " pdb=" N HIS B 41 " pdb=" C HIS B 41 " pdb=" CB HIS B 41 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA PRO A 168 " pdb=" N PRO A 168 " pdb=" C PRO A 168 " pdb=" CB PRO A 168 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.24e-01 ... (remaining 763 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 38 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A 39 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 231 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C ASN A 231 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN A 231 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 232 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 277 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C ASN A 277 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN A 277 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 278 " 0.011 2.00e-02 2.50e+03 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 4 2.55 - 3.14: 3562 3.14 - 3.72: 7054 3.72 - 4.31: 10414 4.31 - 4.90: 17751 Nonbonded interactions: 38785 Sorted by model distance: nonbonded pdb=" O ASN A 277 " pdb=" ND2 ASN A 277 " model vdw 1.960 3.120 nonbonded pdb=" N ASP B 187 " pdb=" OD1 ASP B 187 " model vdw 2.486 3.120 nonbonded pdb=" N ASP A 187 " pdb=" OD1 ASP A 187 " model vdw 2.488 3.120 nonbonded pdb=" NE2 GLN B 69 " pdb=" OE1 GLN B 74 " model vdw 2.546 3.120 nonbonded pdb=" OE2 GLU A 166 " pdb=" N SER B 1 " model vdw 2.560 3.120 ... (remaining 38780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.620 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.005 0.044 4974 Z= 0.323 Angle : 0.813 9.962 6758 Z= 0.441 Chirality : 0.050 0.192 766 Planarity : 0.006 0.095 880 Dihedral : 16.398 84.551 1772 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.24 % Favored : 97.44 % Rotamer: Outliers : 2.61 % Allowed : 20.90 % Favored : 76.49 % 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: -1.27 (0.30), residues: 624 helix: -0.43 (0.36), residues: 168 sheet: -1.09 (0.55), residues: 72 loop : -0.95 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 207 HIS 0.010 0.004 HIS A 41 PHE 0.022 0.003 PHE B 230 TYR 0.025 0.003 TYR A 182 ARG 0.006 0.001 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.6750 (mtm-85) cc_final: 0.6391 (ttp-110) outliers start: 14 outliers final: 3 residues processed: 103 average time/residue: 1.7473 time to fit residues: 184.9933 Evaluate side-chains 86 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 254 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 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 64 HIS A 277 ASN B 64 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4974 Z= 0.193 Angle : 0.566 8.701 6758 Z= 0.294 Chirality : 0.041 0.131 766 Planarity : 0.005 0.068 880 Dihedral : 4.737 33.401 677 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.32 % Allowed : 1.92 % Favored : 97.76 % Rotamer: Outliers : 2.99 % Allowed : 21.46 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.32), residues: 624 helix: 0.97 (0.40), residues: 174 sheet: -0.72 (0.51), residues: 84 loop : -0.50 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 207 HIS 0.007 0.002 HIS A 64 PHE 0.009 0.001 PHE B 230 TYR 0.006 0.001 TYR A 182 ARG 0.004 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 290 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7260 (mt-10) REVERT: B 290 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7230 (mt-10) REVERT: C 7 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7430 (mt0) outliers start: 16 outliers final: 8 residues processed: 90 average time/residue: 1.8339 time to fit residues: 169.6420 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 7 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4974 Z= 0.192 Angle : 0.524 7.942 6758 Z= 0.272 Chirality : 0.041 0.116 766 Planarity : 0.005 0.061 880 Dihedral : 4.307 21.851 675 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.10 % Allowed : 20.15 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.32), residues: 624 helix: 1.21 (0.41), residues: 174 sheet: -0.28 (0.56), residues: 76 loop : -0.56 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 207 HIS 0.006 0.002 HIS B 41 PHE 0.014 0.001 PHE A 223 TYR 0.007 0.001 TYR B 182 ARG 0.007 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: B 279 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6962 (mtp180) outliers start: 22 outliers final: 8 residues processed: 84 average time/residue: 1.8734 time to fit residues: 161.6815 Evaluate side-chains 82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4974 Z= 0.274 Angle : 0.551 7.874 6758 Z= 0.288 Chirality : 0.042 0.117 766 Planarity : 0.005 0.058 880 Dihedral : 4.493 24.689 675 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.36 % Allowed : 19.78 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.32), residues: 624 helix: 1.13 (0.41), residues: 174 sheet: -0.02 (0.58), residues: 76 loop : -0.70 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 207 HIS 0.007 0.002 HIS B 41 PHE 0.015 0.001 PHE A 230 TYR 0.009 0.001 TYR B 237 ARG 0.009 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: B 279 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7050 (mtp180) outliers start: 18 outliers final: 4 residues processed: 81 average time/residue: 1.8137 time to fit residues: 151.1988 Evaluate side-chains 77 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4974 Z= 0.214 Angle : 0.524 7.375 6758 Z= 0.271 Chirality : 0.040 0.117 766 Planarity : 0.005 0.055 880 Dihedral : 4.316 20.988 675 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.92 % Allowed : 18.84 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.32), residues: 624 helix: 1.28 (0.41), residues: 172 sheet: 0.11 (0.58), residues: 76 loop : -0.72 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 207 HIS 0.006 0.002 HIS B 41 PHE 0.011 0.001 PHE B 230 TYR 0.008 0.001 TYR B 182 ARG 0.010 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: B 279 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7041 (mtp180) outliers start: 21 outliers final: 6 residues processed: 81 average time/residue: 1.8553 time to fit residues: 154.6685 Evaluate side-chains 79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 4974 Z= 0.428 Angle : 0.609 7.890 6758 Z= 0.319 Chirality : 0.044 0.135 766 Planarity : 0.005 0.056 880 Dihedral : 4.743 31.436 675 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.66 % Allowed : 18.47 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.32), residues: 624 helix: 1.14 (0.41), residues: 170 sheet: -0.06 (0.56), residues: 76 loop : -0.95 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 207 HIS 0.009 0.002 HIS B 41 PHE 0.017 0.002 PHE B 230 TYR 0.009 0.002 TYR A 182 ARG 0.012 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.581 Fit side-chains REVERT: B 279 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7159 (mtp180) outliers start: 25 outliers final: 5 residues processed: 85 average time/residue: 1.8210 time to fit residues: 159.6893 Evaluate side-chains 71 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4974 Z= 0.187 Angle : 0.529 7.358 6758 Z= 0.269 Chirality : 0.040 0.117 766 Planarity : 0.005 0.052 880 Dihedral : 4.303 20.224 675 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.05 % Allowed : 21.27 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.32), residues: 624 helix: 1.29 (0.41), residues: 172 sheet: -0.00 (0.57), residues: 76 loop : -0.88 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.006 0.001 HIS B 64 PHE 0.009 0.001 PHE A 230 TYR 0.007 0.001 TYR B 182 ARG 0.015 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.561 Fit side-chains REVERT: B 279 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7067 (mtp180) outliers start: 11 outliers final: 6 residues processed: 73 average time/residue: 1.7425 time to fit residues: 130.9213 Evaluate side-chains 70 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 279 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.0570 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 54 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4974 Z= 0.166 Angle : 0.514 7.096 6758 Z= 0.260 Chirality : 0.039 0.117 766 Planarity : 0.005 0.050 880 Dihedral : 4.126 17.136 675 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.05 % Allowed : 21.27 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.32), residues: 624 helix: 1.47 (0.42), residues: 172 sheet: -0.02 (0.57), residues: 76 loop : -0.82 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.004 0.001 HIS B 41 PHE 0.008 0.001 PHE A 230 TYR 0.007 0.001 TYR A 182 ARG 0.015 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.570 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 1.8591 time to fit residues: 134.3462 Evaluate side-chains 69 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.0050 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4974 Z= 0.186 Angle : 0.527 7.274 6758 Z= 0.266 Chirality : 0.040 0.117 766 Planarity : 0.005 0.051 880 Dihedral : 4.077 17.220 674 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.05 % Allowed : 21.64 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.33), residues: 624 helix: 1.53 (0.42), residues: 172 sheet: -0.02 (0.57), residues: 76 loop : -0.80 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 218 HIS 0.007 0.002 HIS B 64 PHE 0.009 0.001 PHE A 230 TYR 0.008 0.001 TYR B 182 ARG 0.017 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.583 Fit side-chains REVERT: D 7 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.6856 (mt0) outliers start: 11 outliers final: 6 residues processed: 72 average time/residue: 1.8619 time to fit residues: 138.1271 Evaluate side-chains 68 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain D residue 7 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS A 189 GLN B 64 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4974 Z= 0.231 Angle : 0.548 7.461 6758 Z= 0.280 Chirality : 0.040 0.118 766 Planarity : 0.005 0.052 880 Dihedral : 4.180 18.201 674 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.24 % Allowed : 21.08 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.33), residues: 624 helix: 1.50 (0.42), residues: 172 sheet: -0.02 (0.57), residues: 76 loop : -0.82 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 207 HIS 0.007 0.002 HIS B 64 PHE 0.011 0.001 PHE A 230 TYR 0.008 0.001 TYR B 182 ARG 0.006 0.001 ARG A 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.534 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 72 average time/residue: 1.8938 time to fit residues: 140.4948 Evaluate side-chains 69 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.0370 chunk 56 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.067953 restraints weight = 8463.375| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.67 r_work: 0.2747 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4974 Z= 0.163 Angle : 0.528 7.517 6758 Z= 0.267 Chirality : 0.039 0.118 766 Planarity : 0.005 0.049 880 Dihedral : 4.028 16.988 674 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.75 % Allowed : 22.57 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.33), residues: 624 helix: 1.61 (0.42), residues: 172 sheet: 0.03 (0.57), residues: 76 loop : -0.74 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.007 0.001 HIS A 64 PHE 0.007 0.001 PHE A 230 TYR 0.007 0.001 TYR A 182 ARG 0.016 0.001 ARG A 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2895.17 seconds wall clock time: 52 minutes 53.85 seconds (3173.85 seconds total)