Starting phenix.real_space_refine on Fri Dec 27 10:50:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cvn_27010/12_2024/8cvn_27010.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cvn_27010/12_2024/8cvn_27010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cvn_27010/12_2024/8cvn_27010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cvn_27010/12_2024/8cvn_27010.map" model { file = "/net/cci-nas-00/data/ceres_data/8cvn_27010/12_2024/8cvn_27010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cvn_27010/12_2024/8cvn_27010.cif" } resolution = 2.4 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= 0.005 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 30 5.16 5 C 2560 2.51 5 N 690 2.21 5 O 770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4054 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 256, 1955 Classifications: {'peptide': 256} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 249} Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 256, 1955 Classifications: {'peptide': 256} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 249} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'NAI': 1, 'SWL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'NAI': 1, 'SWL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.41, per 1000 atoms: 1.33 Number of scatterers: 4054 At special positions: 0 Unit cell: (95.16, 69.16, 56.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 4 15.00 O 770 8.00 N 690 7.00 C 2560 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: 1.09 Conformation dependent library (CDL) restraints added in 496.3 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 928 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 60.5% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 38 through 51 Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.650A pdb=" N TYR A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 127 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 148 through 173 removed outlier: 3.654A pdb=" N LEU A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.520A pdb=" N LEU A 191 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 202 through 205 removed outlier: 4.489A pdb=" N GLU A 205 " --> pdb=" O GLN A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 206 through 218 removed outlier: 4.447A pdb=" N ILE A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 235 removed outlier: 4.179A pdb=" N ILE A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 227 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 29 Processing helix chain 'B' and resid 38 through 51 Processing helix chain 'B' and resid 54 through 56 No H-bonds generated for 'chain 'B' and resid 54 through 56' Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 108 through 123 removed outlier: 3.552A pdb=" N TYR B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 148 through 173 removed outlier: 3.654A pdb=" N LEU B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 195 removed outlier: 3.521A pdb=" N LEU B 191 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 202 through 205 removed outlier: 4.490A pdb=" N GLU B 205 " --> pdb=" O GLN B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 205' Processing helix chain 'B' and resid 206 through 218 removed outlier: 4.447A pdb=" N ILE B 210 " --> pdb=" O TYR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 235 removed outlier: 3.545A pdb=" N GLY B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.488A pdb=" N VAL A 32 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE A 61 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A 34 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 7 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A 89 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 9 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 88 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N MET A 136 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASN A 90 " --> pdb=" O MET A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.586A pdb=" N ASP B 36 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B 7 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL B 89 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU B 9 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 88 " --> pdb=" O ILE B 134 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N MET B 136 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASN B 90 " --> pdb=" O MET B 136 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 625 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: 1.13 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 686 1.30 - 1.43: 998 1.43 - 1.55: 2380 1.55 - 1.68: 16 1.68 - 1.81: 48 Bond restraints: 4128 Sorted by residual: bond pdb=" O1 SWL B 302 " pdb=" S3 SWL B 302 " ideal model delta sigma weight residual 2.267 1.645 0.622 2.00e-02 2.50e+03 9.66e+02 bond pdb=" O1 SWL A 302 " pdb=" S3 SWL A 302 " ideal model delta sigma weight residual 2.267 1.646 0.621 2.00e-02 2.50e+03 9.63e+02 bond pdb=" C SER A 123 " pdb=" O SER A 123 " ideal model delta sigma weight residual 1.234 1.323 -0.089 1.19e-02 7.06e+03 5.54e+01 bond pdb=" C SER B 123 " pdb=" O SER B 123 " ideal model delta sigma weight residual 1.234 1.322 -0.088 1.19e-02 7.06e+03 5.44e+01 bond pdb=" C CYS B 63 " pdb=" N ASP B 64 " ideal model delta sigma weight residual 1.330 1.416 -0.086 1.42e-02 4.96e+03 3.65e+01 ... (remaining 4123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.48: 5494 4.48 - 8.95: 98 8.95 - 13.43: 8 13.43 - 17.90: 0 17.90 - 22.38: 4 Bond angle restraints: 5604 Sorted by residual: angle pdb=" N SER A 123 " pdb=" CA ASER A 123 " pdb=" C SER A 123 " ideal model delta sigma weight residual 110.23 123.25 -13.02 1.45e+00 4.76e-01 8.06e+01 angle pdb=" N SER B 123 " pdb=" CA ASER B 123 " pdb=" C SER B 123 " ideal model delta sigma weight residual 110.23 123.05 -12.82 1.45e+00 4.76e-01 7.81e+01 angle pdb=" C16 SWL B 302 " pdb=" S3 SWL B 302 " pdb=" O1 SWL B 302 " ideal model delta sigma weight residual 88.25 110.63 -22.38 3.00e+00 1.11e-01 5.56e+01 angle pdb=" C16 SWL A 302 " pdb=" S3 SWL A 302 " pdb=" O1 SWL A 302 " ideal model delta sigma weight residual 88.25 110.62 -22.37 3.00e+00 1.11e-01 5.56e+01 angle pdb=" C PRO A 222 " pdb=" CA PRO A 222 " pdb=" CB PRO A 222 " ideal model delta sigma weight residual 110.92 119.76 -8.84 1.22e+00 6.72e-01 5.25e+01 ... (remaining 5599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 2093 16.30 - 32.61: 294 32.61 - 48.91: 88 48.91 - 65.21: 39 65.21 - 81.51: 14 Dihedral angle restraints: 2528 sinusoidal: 1074 harmonic: 1454 Sorted by residual: dihedral pdb=" C PRO A 222 " pdb=" N PRO A 222 " pdb=" CA PRO A 222 " pdb=" CB PRO A 222 " ideal model delta harmonic sigma weight residual -120.70 -133.98 13.28 0 2.50e+00 1.60e-01 2.82e+01 dihedral pdb=" C ASN B 173 " pdb=" N ASN B 173 " pdb=" CA ASN B 173 " pdb=" CB ASN B 173 " ideal model delta harmonic sigma weight residual -122.60 -134.78 12.18 0 2.50e+00 1.60e-01 2.37e+01 dihedral pdb=" C ASN A 173 " pdb=" N ASN A 173 " pdb=" CA ASN A 173 " pdb=" CB ASN A 173 " ideal model delta harmonic sigma weight residual -122.60 -134.33 11.73 0 2.50e+00 1.60e-01 2.20e+01 ... (remaining 2525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.569: 631 0.569 - 1.137: 1 1.137 - 1.706: 0 1.706 - 2.275: 0 2.275 - 2.844: 2 Chirality restraints: 634 Sorted by residual: chirality pdb=" S3 SWL B 302 " pdb=" C10 SWL B 302 " pdb=" C16 SWL B 302 " pdb=" O1 SWL B 302 " both_signs ideal model delta sigma weight residual False -7.07 -4.22 -2.84 2.00e-01 2.50e+01 2.02e+02 chirality pdb=" S3 SWL A 302 " pdb=" C10 SWL A 302 " pdb=" C16 SWL A 302 " pdb=" O1 SWL A 302 " both_signs ideal model delta sigma weight residual False -7.07 -4.23 -2.84 2.00e-01 2.50e+01 2.02e+02 chirality pdb=" CA PRO A 222 " pdb=" N PRO A 222 " pdb=" C PRO A 222 " pdb=" CB PRO A 222 " both_signs ideal model delta sigma weight residual False 2.72 2.10 0.62 2.00e-01 2.50e+01 9.62e+00 ... (remaining 631 not shown) Planarity restraints: 710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 195 " -0.016 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C GLU B 195 " 0.058 2.00e-02 2.50e+03 pdb=" O GLU B 195 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS B 196 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 195 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C GLU A 195 " -0.049 2.00e-02 2.50e+03 pdb=" O GLU A 195 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 196 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 152 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C CYS B 152 " -0.044 2.00e-02 2.50e+03 pdb=" O CYS B 152 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA B 153 " 0.015 2.00e-02 2.50e+03 ... (remaining 707 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 2134 3.01 - 3.48: 3957 3.48 - 3.95: 6653 3.95 - 4.43: 7969 4.43 - 4.90: 12283 Nonbonded interactions: 32996 Sorted by model distance: nonbonded pdb=" O LEU B 178 " pdb=" OD1 ASN B 179 " model vdw 2.536 3.040 nonbonded pdb=" O LEU A 178 " pdb=" OD1 ASN A 179 " model vdw 2.536 3.040 nonbonded pdb=" O GLN B 70 " pdb=" OG1 THR B 74 " model vdw 2.547 3.040 nonbonded pdb=" O TYR A 151 " pdb=" OG SER A 154 " model vdw 2.584 3.040 nonbonded pdb=" O GLN A 70 " pdb=" OG1 THR A 74 " model vdw 2.586 3.040 ... (remaining 32991 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 7.440 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.380 Find NCS groups from input model: 0.110 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:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.018 0.622 4128 Z= 1.124 Angle : 1.467 22.376 5604 Z= 0.909 Chirality : 0.177 2.844 634 Planarity : 0.005 0.034 710 Dihedral : 18.480 81.509 1600 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.21 % Allowed : 19.81 % Favored : 78.99 % Cbeta Deviations : 0.65 % 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: 0.60 (0.37), residues: 508 helix: 1.02 (0.33), residues: 258 sheet: 0.63 (0.47), residues: 108 loop : -0.78 (0.47), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 100 HIS 0.004 0.001 HIS A 156 PHE 0.035 0.003 PHE A 75 TYR 0.019 0.002 TYR A 121 ARG 0.002 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.446 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 77 average time/residue: 1.6059 time to fit residues: 126.8306 Evaluate side-chains 38 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 90 ASN A 148 GLN B 81 HIS B 90 ASN B 148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4128 Z= 0.182 Angle : 0.492 5.937 5604 Z= 0.259 Chirality : 0.042 0.126 634 Planarity : 0.003 0.045 710 Dihedral : 9.406 85.034 686 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.62 % Allowed : 21.50 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.39), residues: 508 helix: 1.95 (0.35), residues: 260 sheet: 0.71 (0.50), residues: 108 loop : -0.02 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 100 HIS 0.003 0.001 HIS A 252 PHE 0.008 0.001 PHE A 82 TYR 0.010 0.001 TYR B 151 ARG 0.005 0.001 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.431 Fit side-chains outliers start: 15 outliers final: 3 residues processed: 49 average time/residue: 1.5060 time to fit residues: 76.1316 Evaluate side-chains 43 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.8383 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4128 Z= 0.174 Angle : 0.444 5.343 5604 Z= 0.238 Chirality : 0.040 0.125 634 Planarity : 0.004 0.043 710 Dihedral : 8.913 85.989 686 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.66 % Allowed : 22.71 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.40), residues: 508 helix: 2.19 (0.36), residues: 260 sheet: 0.59 (0.51), residues: 108 loop : 0.11 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 100 HIS 0.003 0.001 HIS A 252 PHE 0.006 0.001 PHE A 82 TYR 0.007 0.001 TYR B 151 ARG 0.004 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.408 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 53 average time/residue: 1.3433 time to fit residues: 73.7727 Evaluate side-chains 50 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 248 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.0470 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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: 0.8431 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4128 Z= 0.219 Angle : 0.455 5.335 5604 Z= 0.243 Chirality : 0.041 0.124 634 Planarity : 0.004 0.043 710 Dihedral : 8.922 77.645 686 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.66 % Allowed : 23.19 % Favored : 74.15 % 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 (0.40), residues: 508 helix: 2.17 (0.35), residues: 260 sheet: 0.42 (0.50), residues: 108 loop : 0.11 (0.56), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 100 HIS 0.003 0.001 HIS B 156 PHE 0.005 0.001 PHE A 82 TYR 0.007 0.001 TYR B 151 ARG 0.005 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.479 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 1.2299 time to fit residues: 63.8517 Evaluate side-chains 51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 248 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.8476 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4128 Z= 0.310 Angle : 0.495 5.314 5604 Z= 0.260 Chirality : 0.042 0.126 634 Planarity : 0.004 0.044 710 Dihedral : 8.914 75.383 686 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.14 % Allowed : 22.46 % Favored : 74.40 % 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: 1.62 (0.40), residues: 508 helix: 2.02 (0.35), residues: 260 sheet: 0.24 (0.50), residues: 108 loop : 0.08 (0.56), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 100 HIS 0.003 0.001 HIS A 156 PHE 0.005 0.001 PHE B 60 TYR 0.009 0.001 TYR B 216 ARG 0.001 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.443 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 49 average time/residue: 1.3284 time to fit residues: 67.4439 Evaluate side-chains 49 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 248 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4128 Z= 0.205 Angle : 0.432 5.139 5604 Z= 0.230 Chirality : 0.040 0.122 634 Planarity : 0.004 0.044 710 Dihedral : 8.473 67.598 686 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.42 % Allowed : 23.19 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.40), residues: 508 helix: 2.17 (0.35), residues: 260 sheet: 0.07 (0.49), residues: 112 loop : 0.26 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 100 HIS 0.003 0.001 HIS A 252 PHE 0.005 0.001 PHE A 82 TYR 0.007 0.001 TYR B 151 ARG 0.002 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.455 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 46 average time/residue: 1.1938 time to fit residues: 57.0939 Evaluate side-chains 47 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 248 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 22 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.8424 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4128 Z= 0.175 Angle : 0.415 5.121 5604 Z= 0.222 Chirality : 0.039 0.124 634 Planarity : 0.004 0.043 710 Dihedral : 8.177 61.735 686 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.14 % Allowed : 21.74 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.40), residues: 508 helix: 2.28 (0.35), residues: 260 sheet: 0.14 (0.49), residues: 112 loop : 0.20 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 100 HIS 0.003 0.001 HIS A 252 PHE 0.005 0.001 PHE B 82 TYR 0.006 0.001 TYR B 151 ARG 0.003 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.470 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 48 average time/residue: 1.2299 time to fit residues: 61.2990 Evaluate side-chains 45 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 213 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8469 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4128 Z= 0.271 Angle : 0.464 5.204 5604 Z= 0.246 Chirality : 0.041 0.127 634 Planarity : 0.004 0.044 710 Dihedral : 8.511 64.862 686 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.14 % Allowed : 21.50 % Favored : 75.36 % 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: 1.68 (0.40), residues: 508 helix: 2.17 (0.35), residues: 260 sheet: 0.01 (0.49), residues: 112 loop : 0.15 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 100 HIS 0.003 0.001 HIS A 156 PHE 0.005 0.001 PHE B 60 TYR 0.007 0.001 TYR B 151 ARG 0.003 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.408 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 47 average time/residue: 1.2050 time to fit residues: 58.9383 Evaluate side-chains 44 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 248 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.0030 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 0.4268 ------------------------------------------------------------------------------- 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: 0.8416 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4128 Z= 0.157 Angle : 0.406 5.104 5604 Z= 0.217 Chirality : 0.039 0.122 634 Planarity : 0.004 0.044 710 Dihedral : 7.924 58.528 686 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.17 % Allowed : 22.46 % Favored : 75.36 % 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: 1.87 (0.40), residues: 508 helix: 2.38 (0.35), residues: 260 sheet: 0.07 (0.49), residues: 112 loop : 0.15 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 100 HIS 0.003 0.001 HIS B 252 PHE 0.005 0.001 PHE B 82 TYR 0.006 0.001 TYR A 151 ARG 0.003 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.438 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 1.1363 time to fit residues: 51.0063 Evaluate side-chains 45 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 248 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 31 optimal weight: 0.0370 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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: 0.8425 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4128 Z= 0.172 Angle : 0.412 5.102 5604 Z= 0.220 Chirality : 0.039 0.126 634 Planarity : 0.004 0.044 710 Dihedral : 7.861 57.939 686 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.93 % Allowed : 22.71 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.40), residues: 508 helix: 2.39 (0.35), residues: 260 sheet: 0.12 (0.49), residues: 112 loop : 0.11 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 100 HIS 0.003 0.001 HIS A 252 PHE 0.005 0.001 PHE B 82 TYR 0.006 0.001 TYR B 151 ARG 0.004 0.000 ARG B 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.454 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 42 average time/residue: 1.2214 time to fit residues: 53.3491 Evaluate side-chains 45 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 248 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 0.0010 chunk 2 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.3113 r_free = 0.3113 target = 0.089117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.081494 restraints weight = 6024.283| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.03 r_work: 0.2873 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4128 Z= 0.179 Angle : 0.414 5.113 5604 Z= 0.221 Chirality : 0.040 0.124 634 Planarity : 0.004 0.043 710 Dihedral : 7.892 58.444 686 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.93 % Allowed : 22.95 % Favored : 75.12 % 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: 1.88 (0.40), residues: 508 helix: 2.39 (0.35), residues: 260 sheet: 0.09 (0.49), residues: 112 loop : 0.10 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 100 HIS 0.003 0.001 HIS A 252 PHE 0.005 0.001 PHE B 82 TYR 0.007 0.001 TYR B 151 ARG 0.004 0.000 ARG B 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.92 seconds wall clock time: 39 minutes 56.69 seconds (2396.69 seconds total)