Starting phenix.real_space_refine on Sat Apr 26 23:02:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b34_44125/04_2025/9b34_44125.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b34_44125/04_2025/9b34_44125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b34_44125/04_2025/9b34_44125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b34_44125/04_2025/9b34_44125.map" model { file = "/net/cci-nas-00/data/ceres_data/9b34_44125/04_2025/9b34_44125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b34_44125/04_2025/9b34_44125.cif" } resolution = 3.58 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= 0.002 sd= 0.015 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 S 4 5.16 5 C 2281 2.51 5 N 604 2.21 5 O 726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3619 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1806 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1809 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.14, per 1000 atoms: 0.87 Number of scatterers: 3619 At special positions: 0 Unit cell: (63.3889, 57.9941, 93.0603, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 4 16.00 O 726 8.00 N 604 7.00 C 2281 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: 1.25 Conformation dependent library (CDL) restraints added in 395.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 24 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 24 " 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 884 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 10 sheets defined 1.1% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'E' and resid 14 through 18 removed outlier: 3.809A pdb=" N GLY E 18 " --> pdb=" O THR E 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.601A pdb=" N SER E 94 " --> pdb=" O ALA E 211 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY E 92 " --> pdb=" O PHE E 213 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER E 215 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG E 90 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.601A pdb=" N SER E 94 " --> pdb=" O ALA E 211 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY E 92 " --> pdb=" O PHE E 213 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER E 215 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG E 90 " --> pdb=" O SER E 215 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL E 179 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 9 through 10 Processing sheet with id=AA4, first strand: chain 'E' and resid 49 through 54 Processing sheet with id=AA5, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AA6, first strand: chain 'E' and resid 128 through 130 removed outlier: 3.844A pdb=" N THR E 194 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 36 through 39 removed outlier: 4.256A pdb=" N LYS F 36 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 212 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY F 92 " --> pdb=" O PHE F 213 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL F 91 " --> pdb=" O PHE F 175 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU F 174 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 36 through 39 removed outlier: 4.256A pdb=" N LYS F 36 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 212 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY F 92 " --> pdb=" O PHE F 213 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL F 179 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 77 through 78 removed outlier: 3.511A pdb=" N TYR F 77 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA F 50 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE F 52 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR F 194 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER F 108 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU F 198 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE F 106 " --> pdb=" O LEU F 198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 77 through 78 removed outlier: 3.511A pdb=" N TYR F 77 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA F 50 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE F 52 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR F 194 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER F 108 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU F 198 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE F 106 " --> pdb=" O LEU F 198 " (cutoff:3.500A) 110 hydrogen bonds defined for protein. 264 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.95 Time building geometry restraints manager: 1.11 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: 1103 1.34 - 1.45: 640 1.45 - 1.57: 1948 1.57 - 1.69: 0 1.69 - 1.81: 8 Bond restraints: 3699 Sorted by residual: bond pdb=" CA ASP F 208 " pdb=" C ASP F 208 " ideal model delta sigma weight residual 1.521 1.559 -0.037 1.14e-02 7.69e+03 1.08e+01 bond pdb=" C SER F 21 " pdb=" N TYR F 22 " ideal model delta sigma weight residual 1.327 1.296 0.031 1.39e-02 5.18e+03 4.88e+00 bond pdb=" N SER E 119 " pdb=" CA SER E 119 " ideal model delta sigma weight residual 1.457 1.484 -0.026 1.29e-02 6.01e+03 4.19e+00 bond pdb=" CB ASN E 69 " pdb=" CG ASN E 69 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.85e+00 bond pdb=" CA ALA F 186 " pdb=" C ALA F 186 " ideal model delta sigma weight residual 1.523 1.549 -0.025 1.34e-02 5.57e+03 3.60e+00 ... (remaining 3694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.63: 4961 4.63 - 9.27: 74 9.27 - 13.90: 7 13.90 - 18.54: 0 18.54 - 23.17: 2 Bond angle restraints: 5044 Sorted by residual: angle pdb=" N GLY F 48 " pdb=" CA GLY F 48 " pdb=" C GLY F 48 " ideal model delta sigma weight residual 113.18 133.23 -20.05 2.37e+00 1.78e-01 7.16e+01 angle pdb=" N GLY E 48 " pdb=" CA GLY E 48 " pdb=" C GLY E 48 " ideal model delta sigma weight residual 115.33 138.50 -23.17 2.74e+00 1.33e-01 7.15e+01 angle pdb=" N ALA E 207 " pdb=" CA ALA E 207 " pdb=" C ALA E 207 " ideal model delta sigma weight residual 107.20 118.76 -11.56 1.70e+00 3.46e-01 4.62e+01 angle pdb=" N ALA E 186 " pdb=" CA ALA E 186 " pdb=" C ALA E 186 " ideal model delta sigma weight residual 110.80 122.94 -12.14 2.13e+00 2.20e-01 3.25e+01 angle pdb=" N ALA F 186 " pdb=" CA ALA F 186 " pdb=" C ALA F 186 " ideal model delta sigma weight residual 110.80 122.84 -12.04 2.13e+00 2.20e-01 3.20e+01 ... (remaining 5039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 1978 14.84 - 29.69: 146 29.69 - 44.53: 44 44.53 - 59.38: 10 59.38 - 74.22: 4 Dihedral angle restraints: 2182 sinusoidal: 812 harmonic: 1370 Sorted by residual: dihedral pdb=" CA ALA E 207 " pdb=" C ALA E 207 " pdb=" N ASP E 208 " pdb=" CA ASP E 208 " ideal model delta harmonic sigma weight residual 180.00 109.71 70.29 0 5.00e+00 4.00e-02 1.98e+02 dihedral pdb=" CA VAL F 47 " pdb=" C VAL F 47 " pdb=" N GLY F 48 " pdb=" CA GLY F 48 " ideal model delta harmonic sigma weight residual 180.00 117.97 62.03 0 5.00e+00 4.00e-02 1.54e+02 dihedral pdb=" CA VAL E 47 " pdb=" C VAL E 47 " pdb=" N GLY E 48 " pdb=" CA GLY E 48 " ideal model delta harmonic sigma weight residual 180.00 121.49 58.51 0 5.00e+00 4.00e-02 1.37e+02 ... (remaining 2179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 420 0.067 - 0.133: 109 0.133 - 0.200: 34 0.200 - 0.266: 11 0.266 - 0.333: 6 Chirality restraints: 580 Sorted by residual: chirality pdb=" CB VAL F 187 " pdb=" CA VAL F 187 " pdb=" CG1 VAL F 187 " pdb=" CG2 VAL F 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB VAL E 187 " pdb=" CA VAL E 187 " pdb=" CG1 VAL E 187 " pdb=" CG2 VAL E 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB VAL F 75 " pdb=" CA VAL F 75 " pdb=" CG1 VAL F 75 " pdb=" CG2 VAL F 75 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 577 not shown) Planarity restraints: 651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 141 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.35e+00 pdb=" C ILE F 141 " -0.050 2.00e-02 2.50e+03 pdb=" O ILE F 141 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU F 142 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 208 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" CG ASP E 208 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASP E 208 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP E 208 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 118 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.96e+00 pdb=" C ASN F 118 " 0.049 2.00e-02 2.50e+03 pdb=" O ASN F 118 " -0.018 2.00e-02 2.50e+03 pdb=" N SER F 119 " -0.017 2.00e-02 2.50e+03 ... (remaining 648 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 139 2.68 - 3.23: 3433 3.23 - 3.79: 5728 3.79 - 4.34: 7350 4.34 - 4.90: 12555 Nonbonded interactions: 29205 Sorted by model distance: nonbonded pdb=" OD2 ASP E 10 " pdb="ZN ZN E1001 " model vdw 2.121 2.230 nonbonded pdb=" OD1 ASP E 19 " pdb="ZN ZN E1001 " model vdw 2.133 2.230 nonbonded pdb=" OD2 ASP F 10 " pdb="ZN ZN F1001 " model vdw 2.151 2.230 nonbonded pdb=" OD1 ASP F 19 " pdb="ZN ZN F1001 " model vdw 2.181 2.230 nonbonded pdb=" OG SER E 108 " pdb=" OG1 THR E 196 " model vdw 2.261 3.040 ... (remaining 29200 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 'E' selection = (chain 'F' and (resid 1 through 144 or (resid 145 through 146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 147 through 237 or resid 1001 th \ rough 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.810 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 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 : 0.007 0.093 3701 Z= 0.338 Angle : 1.466 23.170 5044 Z= 0.788 Chirality : 0.077 0.333 580 Planarity : 0.009 0.060 651 Dihedral : 12.857 74.220 1298 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 1.91 % Allowed : 23.62 % Favored : 74.47 % Rotamer: Outliers : 0.49 % Allowed : 5.68 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.56 % 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: -5.95 (0.31), residues: 470 helix: None (None), residues: 0 sheet: -4.50 (0.34), residues: 126 loop : -4.04 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP E 182 HIS 0.004 0.001 HIS E 51 PHE 0.036 0.005 PHE E 130 TYR 0.016 0.003 TYR E 176 ARG 0.009 0.002 ARG F 228 Details of bonding type rmsd hydrogen bonds : bond 0.32816 ( 78) hydrogen bonds : angle 13.93349 ( 264) metal coordination : bond 0.02763 ( 2) covalent geometry : bond 0.00655 ( 3699) covalent geometry : angle 1.46591 ( 5044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 ILE cc_start: 0.9158 (tt) cc_final: 0.8886 (mt) REVERT: E 39 LYS cc_start: 0.8538 (tttt) cc_final: 0.8171 (tppp) REVERT: E 53 ILE cc_start: 0.7856 (pp) cc_final: 0.7608 (mt) REVERT: E 55 ASN cc_start: 0.8361 (p0) cc_final: 0.8143 (p0) REVERT: E 126 LEU cc_start: 0.9085 (tp) cc_final: 0.8771 (tp) REVERT: E 158 ARG cc_start: 0.6605 (mtp-110) cc_final: 0.5844 (ptm160) REVERT: E 195 PHE cc_start: 0.7046 (t80) cc_final: 0.6783 (t80) REVERT: E 228 ARG cc_start: 0.7664 (ptp-110) cc_final: 0.5364 (mmt180) REVERT: E 229 LEU cc_start: 0.8479 (mt) cc_final: 0.8220 (mt) REVERT: F 126 LEU cc_start: 0.8408 (tp) cc_final: 0.8126 (tp) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.1789 time to fit residues: 30.2681 Evaluate side-chains 79 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.0470 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 ASN E 162 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F 162 ASN F 180 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.165301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.148383 restraints weight = 6205.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.152795 restraints weight = 3457.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.155678 restraints weight = 2248.806| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3701 Z= 0.185 Angle : 1.024 19.053 5044 Z= 0.520 Chirality : 0.054 0.194 580 Planarity : 0.007 0.052 651 Dihedral : 10.769 51.545 500 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 1.28 % Allowed : 21.49 % Favored : 77.23 % Rotamer: Outliers : 2.72 % Allowed : 16.30 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.56 % 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: -5.47 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -4.06 (0.36), residues: 156 loop : -3.59 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 182 HIS 0.006 0.001 HIS E 121 PHE 0.018 0.002 PHE F 128 TYR 0.016 0.002 TYR E 12 ARG 0.004 0.001 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 78) hydrogen bonds : angle 7.64297 ( 264) metal coordination : bond 0.00344 ( 2) covalent geometry : bond 0.00360 ( 3699) covalent geometry : angle 1.02407 ( 5044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 53 ILE cc_start: 0.7983 (pp) cc_final: 0.7766 (mt) REVERT: E 129 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6696 (ttp) REVERT: E 158 ARG cc_start: 0.6127 (mtp-110) cc_final: 0.5763 (mmm-85) REVERT: E 228 ARG cc_start: 0.7062 (ptp-110) cc_final: 0.5253 (mpt180) REVERT: E 229 LEU cc_start: 0.8192 (mt) cc_final: 0.7986 (mt) REVERT: F 54 TYR cc_start: 0.7228 (t80) cc_final: 0.6752 (t80) REVERT: F 126 LEU cc_start: 0.8516 (tp) cc_final: 0.8225 (tp) outliers start: 11 outliers final: 4 residues processed: 97 average time/residue: 0.1526 time to fit residues: 18.3033 Evaluate side-chains 78 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 180 HIS Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 6 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 51 HIS E 162 ASN F 14 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.142352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.124473 restraints weight = 6230.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.128076 restraints weight = 3796.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.130581 restraints weight = 2628.939| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3701 Z= 0.241 Angle : 0.999 17.307 5044 Z= 0.512 Chirality : 0.054 0.197 580 Planarity : 0.007 0.045 651 Dihedral : 10.678 56.075 500 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 1.28 % Allowed : 22.77 % Favored : 75.96 % Rotamer: Outliers : 5.19 % Allowed : 16.54 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.33 % 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: -5.19 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -3.22 (0.37), residues: 166 loop : -3.78 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP F 182 HIS 0.017 0.003 HIS F 180 PHE 0.021 0.002 PHE E 191 TYR 0.027 0.003 TYR F 12 ARG 0.006 0.001 ARG F 228 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 78) hydrogen bonds : angle 7.28510 ( 264) metal coordination : bond 0.00417 ( 2) covalent geometry : bond 0.00502 ( 3699) covalent geometry : angle 0.99909 ( 5044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 129 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6682 (ttp) REVERT: E 158 ARG cc_start: 0.6180 (mtp-110) cc_final: 0.5833 (mmm-85) REVERT: E 228 ARG cc_start: 0.7508 (ptp-110) cc_final: 0.5643 (mpt180) REVERT: F 94 SER cc_start: 0.8488 (t) cc_final: 0.7688 (p) REVERT: F 145 ASP cc_start: 0.7118 (m-30) cc_final: 0.6905 (t0) REVERT: F 159 VAL cc_start: 0.6819 (p) cc_final: 0.6084 (m) outliers start: 21 outliers final: 12 residues processed: 92 average time/residue: 0.1440 time to fit residues: 16.5509 Evaluate side-chains 86 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.147406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.128979 restraints weight = 6135.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.132671 restraints weight = 3727.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.135358 restraints weight = 2576.074| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3701 Z= 0.157 Angle : 0.927 17.558 5044 Z= 0.468 Chirality : 0.051 0.188 580 Planarity : 0.006 0.041 651 Dihedral : 10.119 52.074 500 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 1.06 % Allowed : 22.34 % Favored : 76.60 % Rotamer: Outliers : 5.19 % Allowed : 19.26 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.11 % 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: -4.86 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -3.02 (0.44), residues: 134 loop : -3.58 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 182 HIS 0.005 0.001 HIS E 121 PHE 0.015 0.002 PHE E 128 TYR 0.007 0.001 TYR F 12 ARG 0.003 0.001 ARG E 90 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 78) hydrogen bonds : angle 6.88307 ( 264) metal coordination : bond 0.00189 ( 2) covalent geometry : bond 0.00328 ( 3699) covalent geometry : angle 0.92731 ( 5044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.426 Fit side-chains REVERT: E 158 ARG cc_start: 0.6057 (mtp-110) cc_final: 0.5735 (mmm-85) REVERT: F 94 SER cc_start: 0.8419 (t) cc_final: 0.7755 (p) REVERT: F 208 ASP cc_start: 0.5519 (t0) cc_final: 0.5001 (m-30) outliers start: 21 outliers final: 13 residues processed: 84 average time/residue: 0.1855 time to fit residues: 20.0328 Evaluate side-chains 84 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 232 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 0.0170 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 ASN E 180 HIS ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.145555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.127625 restraints weight = 6194.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.131223 restraints weight = 3715.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.133635 restraints weight = 2546.339| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3701 Z= 0.169 Angle : 0.939 17.306 5044 Z= 0.473 Chirality : 0.052 0.198 580 Planarity : 0.006 0.040 651 Dihedral : 9.939 49.195 500 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 1.06 % Allowed : 22.98 % Favored : 75.96 % Rotamer: Outliers : 5.19 % Allowed : 19.01 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.11 % 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: -4.58 (0.35), residues: 470 helix: None (None), residues: 0 sheet: -2.80 (0.44), residues: 136 loop : -3.40 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 182 HIS 0.006 0.001 HIS E 121 PHE 0.023 0.002 PHE E 191 TYR 0.013 0.001 TYR F 12 ARG 0.009 0.001 ARG F 33 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 78) hydrogen bonds : angle 6.94857 ( 264) metal coordination : bond 0.00248 ( 2) covalent geometry : bond 0.00353 ( 3699) covalent geometry : angle 0.93891 ( 5044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.535 Fit side-chains REVERT: E 162 ASN cc_start: 0.6278 (OUTLIER) cc_final: 0.6018 (p0) REVERT: E 228 ARG cc_start: 0.7650 (ptp-110) cc_final: 0.5746 (mpt180) REVERT: E 232 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7454 (pp) REVERT: F 94 SER cc_start: 0.8422 (t) cc_final: 0.7697 (p) REVERT: F 208 ASP cc_start: 0.5446 (t0) cc_final: 0.4933 (m-30) outliers start: 21 outliers final: 14 residues processed: 95 average time/residue: 0.1571 time to fit residues: 18.9988 Evaluate side-chains 89 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 232 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 23 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.140023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.121819 restraints weight = 6342.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.125518 restraints weight = 3809.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.128033 restraints weight = 2613.424| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3701 Z= 0.194 Angle : 0.947 15.997 5044 Z= 0.480 Chirality : 0.053 0.188 580 Planarity : 0.006 0.045 651 Dihedral : 9.861 47.796 500 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 1.28 % Allowed : 22.77 % Favored : 75.96 % Rotamer: Outliers : 6.42 % Allowed : 19.51 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % 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: -4.55 (0.35), residues: 470 helix: None (None), residues: 0 sheet: -2.69 (0.44), residues: 144 loop : -3.41 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP E 182 HIS 0.006 0.001 HIS E 121 PHE 0.018 0.002 PHE F 133 TYR 0.020 0.001 TYR F 12 ARG 0.007 0.001 ARG F 33 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 78) hydrogen bonds : angle 7.01895 ( 264) metal coordination : bond 0.00314 ( 2) covalent geometry : bond 0.00404 ( 3699) covalent geometry : angle 0.94709 ( 5044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: E 51 HIS cc_start: 0.6985 (OUTLIER) cc_final: 0.6017 (t70) REVERT: E 208 ASP cc_start: 0.6931 (t0) cc_final: 0.6708 (t0) REVERT: F 94 SER cc_start: 0.8322 (t) cc_final: 0.7784 (p) REVERT: F 145 ASP cc_start: 0.6382 (t0) cc_final: 0.6113 (t0) REVERT: F 208 ASP cc_start: 0.5724 (t0) cc_final: 0.5226 (m-30) REVERT: F 223 SER cc_start: 0.7114 (OUTLIER) cc_final: 0.6820 (t) outliers start: 26 outliers final: 18 residues processed: 92 average time/residue: 0.1244 time to fit residues: 14.6279 Evaluate side-chains 91 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 232 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.146647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.128560 restraints weight = 6316.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132255 restraints weight = 3753.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.134894 restraints weight = 2571.091| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3701 Z= 0.172 Angle : 0.915 14.334 5044 Z= 0.463 Chirality : 0.052 0.174 580 Planarity : 0.006 0.038 651 Dihedral : 9.604 46.235 500 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 1.28 % Allowed : 22.55 % Favored : 76.17 % Rotamer: Outliers : 5.68 % Allowed : 21.73 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % 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: -4.47 (0.35), residues: 470 helix: None (None), residues: 0 sheet: -2.63 (0.45), residues: 140 loop : -3.36 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP E 182 HIS 0.006 0.001 HIS E 121 PHE 0.026 0.002 PHE E 191 TYR 0.011 0.001 TYR F 12 ARG 0.007 0.001 ARG F 33 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 78) hydrogen bonds : angle 6.98292 ( 264) metal coordination : bond 0.00244 ( 2) covalent geometry : bond 0.00359 ( 3699) covalent geometry : angle 0.91520 ( 5044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: E 51 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6068 (t70) REVERT: E 232 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7718 (pp) REVERT: F 94 SER cc_start: 0.8403 (t) cc_final: 0.7884 (p) REVERT: F 145 ASP cc_start: 0.6379 (t0) cc_final: 0.6146 (t0) REVERT: F 208 ASP cc_start: 0.6039 (t0) cc_final: 0.5647 (m-30) REVERT: F 223 SER cc_start: 0.7046 (OUTLIER) cc_final: 0.6671 (t) outliers start: 23 outliers final: 16 residues processed: 88 average time/residue: 0.1412 time to fit residues: 15.8393 Evaluate side-chains 85 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 232 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 0.0370 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.143829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.125118 restraints weight = 6231.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.129029 restraints weight = 3616.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.131824 restraints weight = 2454.744| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3701 Z= 0.152 Angle : 0.902 13.989 5044 Z= 0.452 Chirality : 0.051 0.226 580 Planarity : 0.005 0.039 651 Dihedral : 9.363 45.914 500 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 1.06 % Allowed : 22.77 % Favored : 76.17 % Rotamer: Outliers : 5.68 % Allowed : 21.73 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % 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: -4.35 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.48 (0.46), residues: 140 loop : -3.30 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP E 182 HIS 0.006 0.001 HIS E 121 PHE 0.016 0.002 PHE F 133 TYR 0.006 0.001 TYR F 12 ARG 0.005 0.001 ARG F 33 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 78) hydrogen bonds : angle 6.86784 ( 264) metal coordination : bond 0.00181 ( 2) covalent geometry : bond 0.00321 ( 3699) covalent geometry : angle 0.90250 ( 5044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 51 HIS cc_start: 0.6961 (OUTLIER) cc_final: 0.5981 (t70) REVERT: E 129 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7168 (mtp) REVERT: E 130 PHE cc_start: 0.7455 (m-80) cc_final: 0.7151 (m-80) REVERT: E 213 PHE cc_start: 0.8724 (p90) cc_final: 0.8148 (p90) REVERT: E 232 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7773 (pp) REVERT: F 94 SER cc_start: 0.8623 (t) cc_final: 0.8030 (p) REVERT: F 145 ASP cc_start: 0.6290 (t0) cc_final: 0.6065 (t0) REVERT: F 208 ASP cc_start: 0.5876 (t0) cc_final: 0.5486 (m-30) REVERT: F 223 SER cc_start: 0.7049 (OUTLIER) cc_final: 0.6678 (t) outliers start: 23 outliers final: 15 residues processed: 86 average time/residue: 0.1482 time to fit residues: 16.0328 Evaluate side-chains 89 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 232 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 0.0970 chunk 27 optimal weight: 0.0470 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 0.0570 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 0.0050 overall best weight: 0.1808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 HIS E 153 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.148369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.130185 restraints weight = 6104.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.134004 restraints weight = 3640.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.136514 restraints weight = 2506.494| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.7405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3701 Z= 0.138 Angle : 0.886 14.248 5044 Z= 0.440 Chirality : 0.051 0.241 580 Planarity : 0.005 0.040 651 Dihedral : 8.895 44.951 500 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.85 % Allowed : 21.28 % Favored : 77.87 % Rotamer: Outliers : 4.20 % Allowed : 23.21 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % 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: -4.25 (0.37), residues: 470 helix: None (None), residues: 0 sheet: -2.51 (0.46), residues: 142 loop : -3.18 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP E 182 HIS 0.005 0.001 HIS E 121 PHE 0.029 0.002 PHE E 191 TYR 0.012 0.001 TYR F 12 ARG 0.003 0.001 ARG F 33 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 78) hydrogen bonds : angle 6.81105 ( 264) metal coordination : bond 0.00063 ( 2) covalent geometry : bond 0.00293 ( 3699) covalent geometry : angle 0.88644 ( 5044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: E 51 HIS cc_start: 0.6842 (OUTLIER) cc_final: 0.5712 (t70) REVERT: E 232 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7721 (pp) REVERT: F 60 ARG cc_start: 0.7207 (mmm160) cc_final: 0.6663 (mtm-85) REVERT: F 94 SER cc_start: 0.8211 (t) cc_final: 0.7505 (p) REVERT: F 145 ASP cc_start: 0.6071 (t0) cc_final: 0.5867 (t0) REVERT: F 208 ASP cc_start: 0.5654 (t0) cc_final: 0.5163 (m-30) outliers start: 17 outliers final: 10 residues processed: 79 average time/residue: 0.1523 time to fit residues: 15.2942 Evaluate side-chains 71 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.140480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.122318 restraints weight = 6349.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.125920 restraints weight = 3885.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.128449 restraints weight = 2718.195| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.7522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3701 Z= 0.199 Angle : 0.930 13.135 5044 Z= 0.470 Chirality : 0.052 0.195 580 Planarity : 0.006 0.035 651 Dihedral : 9.256 44.642 500 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.85 % Allowed : 23.62 % Favored : 75.53 % Rotamer: Outliers : 3.21 % Allowed : 26.91 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % 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: -4.27 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.39 (0.46), residues: 140 loop : -3.27 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP E 182 HIS 0.005 0.001 HIS E 121 PHE 0.020 0.002 PHE F 191 TYR 0.033 0.002 TYR F 12 ARG 0.004 0.001 ARG E 158 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 78) hydrogen bonds : angle 6.99357 ( 264) metal coordination : bond 0.00287 ( 2) covalent geometry : bond 0.00417 ( 3699) covalent geometry : angle 0.93031 ( 5044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 51 HIS cc_start: 0.7012 (OUTLIER) cc_final: 0.6059 (t70) REVERT: E 130 PHE cc_start: 0.7597 (m-80) cc_final: 0.7295 (m-80) REVERT: E 213 PHE cc_start: 0.8813 (p90) cc_final: 0.8173 (p90) REVERT: F 145 ASP cc_start: 0.6115 (t0) cc_final: 0.5908 (t0) REVERT: F 208 ASP cc_start: 0.6229 (t0) cc_final: 0.5825 (m-30) outliers start: 13 outliers final: 11 residues processed: 78 average time/residue: 0.1545 time to fit residues: 14.9516 Evaluate side-chains 80 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 20 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.145231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.127479 restraints weight = 6139.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.131181 restraints weight = 3655.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.133623 restraints weight = 2512.974| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.7690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3701 Z= 0.165 Angle : 0.910 13.723 5044 Z= 0.456 Chirality : 0.052 0.222 580 Planarity : 0.005 0.036 651 Dihedral : 9.139 44.271 500 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.85 % Allowed : 22.77 % Favored : 76.38 % Rotamer: Outliers : 2.72 % Allowed : 27.41 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % 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: -4.32 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.47 (0.47), residues: 136 loop : -3.28 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP E 182 HIS 0.007 0.001 HIS E 121 PHE 0.025 0.002 PHE E 191 TYR 0.022 0.001 TYR F 12 ARG 0.005 0.001 ARG F 33 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 78) hydrogen bonds : angle 6.81017 ( 264) metal coordination : bond 0.00217 ( 2) covalent geometry : bond 0.00349 ( 3699) covalent geometry : angle 0.90969 ( 5044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1671.37 seconds wall clock time: 29 minutes 40.49 seconds (1780.49 seconds total)