Starting phenix.real_space_refine on Wed Jul 1 22:46:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b34_44125/07_2026/9b34_44125.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b34_44125/07_2026/9b34_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b34_44125/07_2026/9b34_44125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b34_44125/07_2026/9b34_44125.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b34_44125/07_2026/9b34_44125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b34_44125/07_2026/9b34_44125.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 0.94, per 1000 atoms: 0.26 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: 0.18 Conformation dependent library (CDL) restraints added in 87.6 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: 0.11 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: 0.45 Time building geometry restraints manager: 0.25 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 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.210 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.009 0.002 ARG F 228 TYR 0.016 0.003 TYR E 176 PHE 0.036 0.005 PHE E 130 TRP 0.035 0.005 TRP E 182 HIS 0.004 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.34 ( 3699) covalent geometry : angle 1.46591 / 0.79 ( 5044) hydrogen bonds : bond 0.32816 / 22.12 ( 78) hydrogen bonds : angle 13.93349 / 9.63 ( 264) metal coordination : bond 0.02763 / 1.34 ( 2) *********************** 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 : 0.132 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: 0.0618 time to fit residues: 10.6075 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 : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.0670 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 14 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.163266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.146229 restraints weight = 6160.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.150579 restraints weight = 3444.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.153433 restraints weight = 2253.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.155383 restraints weight = 1611.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.156744 restraints weight = 1232.007| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3510 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= 0.188 Angle : 1.037 19.069 5044 Z= 0.527 Chirality : 0.055 0.207 580 Planarity : 0.007 0.052 651 Dihedral : 10.881 53.195 500 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 1.28 % Allowed : 22.13 % Favored : 76.60 % Rotamer: Outliers : 3.46 % Allowed : 15.06 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.78 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.51 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -4.09 (0.35), residues: 156 loop : -3.62 (0.30), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 33 TYR 0.015 0.002 TYR E 12 PHE 0.018 0.003 PHE F 128 TRP 0.029 0.002 TRP E 182 HIS 0.005 0.001 HIS E 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 ( 3699) covalent geometry : angle 1.03703 / 0.53 ( 5044) hydrogen bonds : bond 0.04748 / 3.06 ( 78) hydrogen bonds : angle 7.69137 / 5.39 ( 264) metal coordination : bond 0.00094 / 0.04 ( 2) *********************** 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 112 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 129 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6836 (ttp) REVERT: E 158 ARG cc_start: 0.6073 (mtp-110) cc_final: 0.5681 (mmm-85) REVERT: E 228 ARG cc_start: 0.6956 (ptp-110) cc_final: 0.5096 (mpt180) REVERT: E 229 LEU cc_start: 0.8273 (mt) cc_final: 0.8057 (mt) REVERT: F 54 TYR cc_start: 0.7236 (t80) cc_final: 0.6900 (t80) REVERT: F 126 LEU cc_start: 0.8558 (tp) cc_final: 0.8255 (tp) REVERT: F 208 ASP cc_start: 0.4110 (t0) cc_final: 0.3825 (t0) outliers start: 14 outliers final: 6 residues processed: 106 average time/residue: 0.0428 time to fit residues: 5.7078 Evaluate side-chains 82 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 SER 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 220 SER 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 14 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 51 HIS E 153 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 = 0.3945 r_free = 0.3945 target = 0.142080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123809 restraints weight = 6276.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.127606 restraints weight = 3797.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.130244 restraints weight = 2615.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.132001 restraints weight = 1958.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.133424 restraints weight = 1556.578| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 3701 Z= 0.235 Angle : 1.005 17.524 5044 Z= 0.518 Chirality : 0.054 0.196 580 Planarity : 0.006 0.046 651 Dihedral : 10.631 55.114 500 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 1.28 % Allowed : 22.55 % Favored : 76.17 % Rotamer: Outliers : 4.69 % Allowed : 15.56 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.23 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -3.23 (0.37), residues: 166 loop : -3.83 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 228 TYR 0.021 0.002 TYR F 12 PHE 0.021 0.002 PHE E 191 TRP 0.018 0.003 TRP F 182 HIS 0.015 0.002 HIS F 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 ( 3699) covalent geometry : angle 1.00454 / 0.52 ( 5044) hydrogen bonds : bond 0.04404 / 2.89 ( 78) hydrogen bonds : angle 7.28595 / 5.15 ( 264) metal coordination : bond 0.00442 / 0.22 ( 2) *********************** 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 108 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 40 TRP cc_start: 0.8210 (t60) cc_final: 0.7897 (t60) REVERT: E 41 ASN cc_start: 0.8494 (t0) cc_final: 0.8145 (t0) REVERT: E 158 ARG cc_start: 0.5916 (mtp-110) cc_final: 0.5635 (mmm-85) REVERT: E 228 ARG cc_start: 0.7382 (ptp-110) cc_final: 0.5441 (mpt180) REVERT: F 94 SER cc_start: 0.8569 (t) cc_final: 0.7826 (p) REVERT: F 159 VAL cc_start: 0.6801 (p) cc_final: 0.6090 (m) outliers start: 19 outliers final: 10 residues processed: 99 average time/residue: 0.0464 time to fit residues: 5.8294 Evaluate side-chains 90 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 83 ASN Chi-restraints excluded: chain E residue 153 ASN Chi-restraints excluded: chain E residue 210 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 180 HIS F 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.141915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.123445 restraints weight = 6072.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.127041 restraints weight = 3701.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.129433 restraints weight = 2571.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.131147 restraints weight = 1955.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.132570 restraints weight = 1576.115| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.5666 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= 0.214 Angle : 0.976 17.409 5044 Z= 0.499 Chirality : 0.053 0.187 580 Planarity : 0.006 0.040 651 Dihedral : 10.431 55.318 500 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 1.28 % Allowed : 24.68 % Favored : 74.04 % Rotamer: Outliers : 5.19 % Allowed : 18.77 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -3.23 (0.41), residues: 138 loop : -3.64 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 60 TYR 0.019 0.002 TYR F 12 PHE 0.015 0.002 PHE E 130 TRP 0.023 0.002 TRP E 182 HIS 0.005 0.001 HIS E 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 ( 3699) covalent geometry : angle 0.97608 / 0.50 ( 5044) hydrogen bonds : bond 0.03870 / 2.54 ( 78) hydrogen bonds : angle 7.06416 / 5.00 ( 264) metal coordination : bond 0.00382 / 0.20 ( 2) *********************** 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 103 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 158 ARG cc_start: 0.5918 (mtp-110) cc_final: 0.5517 (mmm-85) REVERT: F 87 GLU cc_start: 0.6722 (tp30) cc_final: 0.6350 (tp30) REVERT: F 94 SER cc_start: 0.8479 (t) cc_final: 0.7843 (p) REVERT: F 208 ASP cc_start: 0.6187 (t0) cc_final: 0.5666 (m-30) REVERT: F 221 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8497 (pt) outliers start: 21 outliers final: 15 residues processed: 96 average time/residue: 0.0399 time to fit residues: 5.0136 Evaluate side-chains 91 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 153 ASN 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 110 SER Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 221 ILE 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 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.0980 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 153 ASN E 162 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 = 0.3935 r_free = 0.3935 target = 0.142572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.123826 restraints weight = 6146.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.127516 restraints weight = 3713.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.130156 restraints weight = 2580.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.131934 restraints weight = 1939.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.133448 restraints weight = 1549.157| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3701 Z= 0.189 Angle : 0.968 17.768 5044 Z= 0.487 Chirality : 0.054 0.195 580 Planarity : 0.006 0.040 651 Dihedral : 10.159 50.825 500 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 1.28 % Allowed : 24.68 % Favored : 74.04 % Rotamer: Outliers : 6.91 % Allowed : 18.27 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.35), residues: 470 helix: None (None), residues: 0 sheet: -3.03 (0.43), residues: 140 loop : -3.48 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 158 TYR 0.016 0.002 TYR F 12 PHE 0.024 0.002 PHE E 191 TRP 0.031 0.002 TRP E 182 HIS 0.005 0.001 HIS E 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 ( 3699) covalent geometry : angle 0.96761 / 0.49 ( 5044) hydrogen bonds : bond 0.03749 / 2.45 ( 78) hydrogen bonds : angle 7.09734 / 4.98 ( 264) metal coordination : bond 0.00327 / 0.17 ( 2) *********************** 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 108 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 41 ASN cc_start: 0.8521 (t0) cc_final: 0.8288 (t0) REVERT: E 129 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.7024 (ttt) REVERT: E 208 ASP cc_start: 0.7211 (t70) cc_final: 0.6529 (t70) REVERT: F 93 LEU cc_start: 0.8777 (mp) cc_final: 0.8567 (mm) REVERT: F 94 SER cc_start: 0.8467 (t) cc_final: 0.7820 (p) REVERT: F 208 ASP cc_start: 0.6016 (t0) cc_final: 0.5746 (m-30) REVERT: F 221 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8497 (pt) REVERT: F 223 SER cc_start: 0.7312 (OUTLIER) cc_final: 0.7031 (t) outliers start: 28 outliers final: 18 residues processed: 97 average time/residue: 0.0410 time to fit residues: 5.1116 Evaluate side-chains 97 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 62 SER 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 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 106 ILE Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 221 ILE 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 9 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.0020 chunk 17 optimal weight: 0.5980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.143908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.125210 restraints weight = 6170.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.129081 restraints weight = 3701.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131789 restraints weight = 2541.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.133593 restraints weight = 1899.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.135005 restraints weight = 1515.778| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3701 Z= 0.164 Angle : 0.937 16.306 5044 Z= 0.477 Chirality : 0.053 0.183 580 Planarity : 0.006 0.039 651 Dihedral : 9.796 46.877 500 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 1.28 % Allowed : 23.62 % Favored : 75.11 % Rotamer: Outliers : 6.91 % Allowed : 19.26 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.56 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.68 (0.45), residues: 140 loop : -3.43 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 158 TYR 0.010 0.001 TYR F 12 PHE 0.017 0.002 PHE F 191 TRP 0.034 0.002 TRP E 182 HIS 0.006 0.001 HIS F 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 3699) covalent geometry : angle 0.93692 / 0.48 ( 5044) hydrogen bonds : bond 0.03614 / 2.37 ( 78) hydrogen bonds : angle 6.92601 / 4.89 ( 264) metal coordination : bond 0.00201 / 0.10 ( 2) *********************** 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 103 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6033 (t70) REVERT: E 129 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6922 (mtp) REVERT: E 208 ASP cc_start: 0.6560 (t70) cc_final: 0.5777 (t70) REVERT: E 232 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7764 (pp) REVERT: F 60 ARG cc_start: 0.7142 (ttp-110) cc_final: 0.6934 (ttp-110) REVERT: F 94 SER cc_start: 0.8462 (t) cc_final: 0.7964 (p) REVERT: F 208 ASP cc_start: 0.6019 (t0) cc_final: 0.5732 (m-30) REVERT: F 221 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8396 (pt) REVERT: F 223 SER cc_start: 0.6924 (OUTLIER) cc_final: 0.6632 (t) outliers start: 28 outliers final: 17 residues processed: 92 average time/residue: 0.0381 time to fit residues: 4.5166 Evaluate side-chains 94 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 62 SER 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 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 107 LEU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 221 ILE 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 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.142127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.123632 restraints weight = 6203.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.127336 restraints weight = 3731.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.129850 restraints weight = 2583.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131694 restraints weight = 1952.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.132790 restraints weight = 1570.444| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.6810 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= 0.207 Angle : 0.951 14.595 5044 Z= 0.485 Chirality : 0.054 0.220 580 Planarity : 0.006 0.039 651 Dihedral : 9.880 47.723 500 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 1.06 % Allowed : 24.26 % Favored : 74.68 % Rotamer: Outliers : 7.16 % Allowed : 20.00 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.59 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.66 (0.44), residues: 144 loop : -3.47 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 158 TYR 0.017 0.002 TYR F 12 PHE 0.024 0.003 PHE E 191 TRP 0.040 0.003 TRP E 182 HIS 0.006 0.001 HIS E 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 ( 3699) covalent geometry : angle 0.95065 / 0.48 ( 5044) hydrogen bonds : bond 0.03552 / 2.34 ( 78) hydrogen bonds : angle 7.14145 / 5.00 ( 264) metal coordination : bond 0.00376 / 0.19 ( 2) *********************** 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 103 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 HIS cc_start: 0.6967 (OUTLIER) cc_final: 0.6050 (t70) REVERT: E 208 ASP cc_start: 0.6327 (t70) cc_final: 0.5684 (t70) REVERT: E 232 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7790 (pp) REVERT: F 60 ARG cc_start: 0.7274 (ttp-110) cc_final: 0.7070 (ttp-170) REVERT: F 94 SER cc_start: 0.8424 (t) cc_final: 0.7902 (p) REVERT: F 208 ASP cc_start: 0.6028 (t0) cc_final: 0.5685 (m-30) REVERT: F 223 SER cc_start: 0.7165 (OUTLIER) cc_final: 0.6879 (t) outliers start: 29 outliers final: 19 residues processed: 93 average time/residue: 0.0454 time to fit residues: 5.4529 Evaluate side-chains 91 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 53 ILE 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 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 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 74 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 176 TYR 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 38 optimal weight: 5.9990 chunk 45 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 162 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.143773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.125559 restraints weight = 6150.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.129166 restraints weight = 3674.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.131778 restraints weight = 2537.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.133542 restraints weight = 1904.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.134905 restraints weight = 1529.843| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.7110 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= 0.166 Angle : 0.933 14.457 5044 Z= 0.470 Chirality : 0.053 0.220 580 Planarity : 0.006 0.040 651 Dihedral : 9.585 45.848 500 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.85 % Allowed : 23.62 % Favored : 75.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.50 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.53 (0.46), residues: 140 loop : -3.44 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 33 TYR 0.009 0.001 TYR F 12 PHE 0.021 0.002 PHE F 191 TRP 0.042 0.002 TRP E 182 HIS 0.005 0.001 HIS E 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 3699) covalent geometry : angle 0.93286 / 0.47 ( 5044) hydrogen bonds : bond 0.03405 / 2.18 ( 78) hydrogen bonds : angle 7.07809 / 4.93 ( 264) metal coordination : bond 0.00238 / 0.12 ( 2) *********************** 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 91 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.5974 (t70) REVERT: E 208 ASP cc_start: 0.6369 (t70) cc_final: 0.5773 (t70) REVERT: F 60 ARG cc_start: 0.7237 (ttp-110) cc_final: 0.6934 (ttp-110) REVERT: F 94 SER cc_start: 0.8498 (t) cc_final: 0.7983 (p) REVERT: F 208 ASP cc_start: 0.5846 (t0) cc_final: 0.5633 (m-30) REVERT: F 223 SER cc_start: 0.6967 (OUTLIER) cc_final: 0.6659 (t) outliers start: 23 outliers final: 18 residues processed: 84 average time/residue: 0.0510 time to fit residues: 5.5014 Evaluate side-chains 83 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 62 SER 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 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 74 THR Chi-restraints excluded: chain F residue 142 LEU 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 44 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 162 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.141377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122758 restraints weight = 6132.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.126468 restraints weight = 3729.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.128996 restraints weight = 2599.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.130786 restraints weight = 1990.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.132248 restraints weight = 1605.231| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.7346 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= 0.175 Angle : 0.928 13.862 5044 Z= 0.469 Chirality : 0.053 0.223 580 Planarity : 0.006 0.040 651 Dihedral : 9.417 45.966 500 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.85 % Allowed : 22.98 % Favored : 76.17 % Rotamer: Outliers : 5.93 % Allowed : 22.22 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.46 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.47 (0.47), residues: 140 loop : -3.43 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 33 TYR 0.010 0.001 TYR F 12 PHE 0.027 0.002 PHE E 191 TRP 0.044 0.002 TRP E 182 HIS 0.005 0.001 HIS E 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 3699) covalent geometry : angle 0.92812 / 0.47 ( 5044) hydrogen bonds : bond 0.03330 / 2.15 ( 78) hydrogen bonds : angle 7.08294 / 4.94 ( 264) metal coordination : bond 0.00252 / 0.13 ( 2) *********************** 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 93 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6080 (t70) REVERT: E 162 ASN cc_start: 0.5003 (OUTLIER) cc_final: 0.4505 (p0) REVERT: E 208 ASP cc_start: 0.6347 (t70) cc_final: 0.5744 (t70) REVERT: E 232 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7833 (pp) REVERT: F 94 SER cc_start: 0.8518 (t) cc_final: 0.8066 (p) REVERT: F 223 SER cc_start: 0.7110 (OUTLIER) cc_final: 0.6754 (t) outliers start: 24 outliers final: 18 residues processed: 87 average time/residue: 0.0542 time to fit residues: 6.0427 Evaluate side-chains 87 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 53 ILE 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 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 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 74 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 179 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 HIS ** 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 = 0.3956 r_free = 0.3956 target = 0.144282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.125981 restraints weight = 6178.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129567 restraints weight = 3683.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.132121 restraints weight = 2551.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.133854 restraints weight = 1922.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.135304 restraints weight = 1539.866| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.7448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 3701 Z= 0.252 Angle : 1.426 59.197 5044 Z= 0.813 Chirality : 0.055 0.350 580 Planarity : 0.006 0.039 651 Dihedral : 9.442 45.921 500 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 1.06 % Allowed : 22.98 % Favored : 75.96 % Rotamer: Outliers : 5.93 % Allowed : 22.22 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.47 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.47 (0.47), residues: 140 loop : -3.45 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 33 TYR 0.010 0.001 TYR F 12 PHE 0.022 0.002 PHE F 191 TRP 0.041 0.003 TRP E 182 HIS 0.005 0.001 HIS E 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.25 ( 3699) covalent geometry : angle 1.42552 / 0.81 ( 5044) hydrogen bonds : bond 0.03339 / 2.14 ( 78) hydrogen bonds : angle 7.08627 / 4.94 ( 264) metal coordination : bond 0.00170 / 0.09 ( 2) ********************** 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 89 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 HIS cc_start: 0.7078 (OUTLIER) cc_final: 0.6075 (t70) REVERT: E 208 ASP cc_start: 0.6296 (t70) cc_final: 0.5671 (t70) REVERT: E 232 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7860 (pp) REVERT: F 94 SER cc_start: 0.8545 (t) cc_final: 0.8055 (p) REVERT: F 208 ASP cc_start: 0.6184 (OUTLIER) cc_final: 0.5594 (m-30) REVERT: F 223 SER cc_start: 0.7102 (OUTLIER) cc_final: 0.6757 (t) outliers start: 24 outliers final: 20 residues processed: 80 average time/residue: 0.0454 time to fit residues: 4.6705 Evaluate side-chains 86 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 62 SER 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 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 74 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 208 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 50.0000 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 162 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 = 0.3960 r_free = 0.3960 target = 0.144635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.126675 restraints weight = 6041.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.130127 restraints weight = 3636.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.132499 restraints weight = 2526.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.134360 restraints weight = 1924.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.135732 restraints weight = 1532.617| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.7465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 3701 Z= 0.252 Angle : 1.426 59.197 5044 Z= 0.813 Chirality : 0.055 0.350 580 Planarity : 0.006 0.039 651 Dihedral : 9.442 45.921 500 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 1.06 % Allowed : 22.98 % Favored : 75.96 % Rotamer: Outliers : 5.93 % Allowed : 23.21 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.47 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.47 (0.47), residues: 140 loop : -3.45 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 33 TYR 0.010 0.001 TYR F 12 PHE 0.022 0.002 PHE F 191 TRP 0.041 0.003 TRP E 182 HIS 0.005 0.001 HIS E 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.25 ( 3699) covalent geometry : angle 1.42552 / 0.81 ( 5044) hydrogen bonds : bond 0.03339 / 2.14 ( 78) hydrogen bonds : angle 7.08627 / 4.94 ( 264) metal coordination : bond 0.00170 / 0.09 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 675.21 seconds wall clock time: 12 minutes 20.37 seconds (740.37 seconds total)