Starting phenix.real_space_refine on Thu Oct 22 20:42:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hbv_52031/10_2026/9hbv_52031.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hbv_52031/10_2026/9hbv_52031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hbv_52031/10_2026/9hbv_52031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hbv_52031/10_2026/9hbv_52031.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hbv_52031/10_2026/9hbv_52031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hbv_52031/10_2026/9hbv_52031.map" } resolution = 3.38 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= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 34 5.16 5 C 3313 2.51 5 N 966 2.21 5 O 1062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5405 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2244 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 148 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "O" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'RNA': 10} Modifications used: {'rna2p': 1, 'rna3p': 9} Link IDs: {'rna2p': 1, 'rna3p': 8} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Chain: "N" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 390 Classifications: {'RNA': 20} Modifications used: {'rna2p': 1, 'rna3p': 19} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Time building chain proxies: 1.05, per 1000 atoms: 0.19 Number of scatterers: 5405 At special positions: 0 Unit cell: (83.022, 99.462, 78.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 30 15.00 O 1062 8.00 N 966 7.00 C 3313 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: 0.46 Conformation dependent library (CDL) restraints added in 201.1 milliseconds 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 51.7% alpha, 4.8% beta 0 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'C' and resid 36 through 51 Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 58 through 74 Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.640A pdb=" N VAL C 128 " --> pdb=" O CYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 142 Processing helix chain 'C' and resid 143 through 173 removed outlier: 3.503A pdb=" N LEU C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 205 through 214 removed outlier: 3.531A pdb=" N ALA C 209 " --> pdb=" O GLY C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 249 through 258 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.835A pdb=" N LEU C 266 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 340 through 349 Processing helix chain 'D' and resid 36 through 51 Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 58 through 74 Processing helix chain 'D' and resid 88 through 101 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.657A pdb=" N TYR D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL D 128 " --> pdb=" O CYS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 142 Processing helix chain 'D' and resid 143 through 175 removed outlier: 4.195A pdb=" N VAL D 174 " --> pdb=" O TYR D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 193 through 200 Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.732A pdb=" N LEU D 266 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 312 removed outlier: 3.770A pdb=" N GLY D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 349 removed outlier: 3.521A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 109 through 110 removed outlier: 3.670A pdb=" N LEU C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AA3, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AA4, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'D' and resid 270 through 271 Processing sheet with id=AA6, first strand: chain 'D' and resid 285 through 286 removed outlier: 3.648A pdb=" N LEU D 285 " --> pdb=" O GLN D 326 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN D 326 " --> pdb=" O LEU D 285 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 0.81 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1683 1.34 - 1.46: 1342 1.46 - 1.58: 2433 1.58 - 1.69: 57 1.69 - 1.81: 46 Bond restraints: 5561 Sorted by residual: bond pdb=" N3 Y5P N 12 " pdb=" C4 Y5P N 12 " ideal model delta sigma weight residual 1.458 1.334 0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" N3 Y5P N 14 " pdb=" C4 Y5P N 14 " ideal model delta sigma weight residual 1.458 1.335 0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C2 Y5P N 28 " pdb=" N3 Y5P N 28 " ideal model delta sigma weight residual 1.268 1.374 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C2 Y5P N 10 " pdb=" N3 Y5P N 10 " ideal model delta sigma weight residual 1.268 1.373 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C2 Y5P N 11 " pdb=" N3 Y5P N 11 " ideal model delta sigma weight residual 1.268 1.373 -0.105 2.00e-02 2.50e+03 2.74e+01 ... (remaining 5556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 7402 2.40 - 4.79: 130 4.79 - 7.19: 40 7.19 - 9.59: 17 9.59 - 11.99: 11 Bond angle restraints: 7600 Sorted by residual: angle pdb=" N1 Y5P N 39 " pdb=" C2 Y5P N 39 " pdb=" N3 Y5P N 39 " ideal model delta sigma weight residual 126.68 114.69 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" N1 Y5P N 37 " pdb=" C2 Y5P N 37 " pdb=" N3 Y5P N 37 " ideal model delta sigma weight residual 126.68 114.74 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" N1 Y5P O 12 " pdb=" C2 Y5P O 12 " pdb=" N3 Y5P O 12 " ideal model delta sigma weight residual 126.68 114.79 11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N1 Y5P N 38 " pdb=" C2 Y5P N 38 " pdb=" N3 Y5P N 38 " ideal model delta sigma weight residual 126.68 114.80 11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N1 Y5P O 8 " pdb=" C2 Y5P O 8 " pdb=" N3 Y5P O 8 " ideal model delta sigma weight residual 126.68 114.86 11.82 3.00e+00 1.11e-01 1.55e+01 ... (remaining 7595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 3640 35.19 - 70.37: 141 70.37 - 105.56: 86 105.56 - 140.74: 1 140.74 - 175.93: 1 Dihedral angle restraints: 3869 sinusoidal: 2080 harmonic: 1789 Sorted by residual: dihedral pdb=" P Y5P N 37 " pdb=" O5' Y5P N 37 " pdb=" C5' Y5P N 37 " pdb=" C4' Y5P N 37 " ideal model delta sinusoidal sigma weight residual 248.90 72.97 175.93 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" P Y5P O 8 " pdb=" O5' Y5P O 8 " pdb=" C5' Y5P O 8 " pdb=" C4' Y5P O 8 " ideal model delta sinusoidal sigma weight residual 248.90 138.19 110.71 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" CB GLU C 95 " pdb=" CG GLU C 95 " pdb=" CD GLU C 95 " pdb=" OE1 GLU C 95 " ideal model delta sinusoidal sigma weight residual 0.00 89.91 -89.91 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 3866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 569 0.028 - 0.056: 212 0.056 - 0.084: 35 0.084 - 0.111: 25 0.111 - 0.139: 14 Chirality restraints: 855 Sorted by residual: chirality pdb=" CA ILE C 230 " pdb=" N ILE C 230 " pdb=" C ILE C 230 " pdb=" CB ILE C 230 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE D 230 " pdb=" N ILE D 230 " pdb=" C ILE D 230 " pdb=" CB ILE D 230 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA VAL D 128 " pdb=" N VAL D 128 " pdb=" C VAL D 128 " pdb=" CB VAL D 128 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 852 not shown) Planarity restraints: 876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 230 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO D 231 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO D 231 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 231 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 47 " 0.005 2.00e-02 2.50e+03 9.93e-03 9.85e-01 pdb=" C GLY C 47 " -0.017 2.00e-02 2.50e+03 pdb=" O GLY C 47 " 0.006 2.00e-02 2.50e+03 pdb=" N HIS C 48 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 103 " -0.016 5.00e-02 4.00e+02 2.41e-02 9.31e-01 pdb=" N PRO C 104 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " -0.013 5.00e-02 4.00e+02 ... (remaining 873 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 37 2.56 - 3.14: 4239 3.14 - 3.73: 8310 3.73 - 4.31: 11299 4.31 - 4.90: 18377 Nonbonded interactions: 42262 Sorted by model distance: nonbonded pdb=" OG1 THR C 182 " pdb=" OD2 ASP C 185 " model vdw 1.973 3.040 nonbonded pdb=" O ASP C 185 " pdb=" OH TYR C 191 " model vdw 2.084 3.040 nonbonded pdb=" O2' P5P N 33 " pdb=" OP1 P5P N 34 " model vdw 2.162 3.040 nonbonded pdb=" O SER C 113 " pdb=" OG SER C 113 " model vdw 2.180 3.040 nonbonded pdb=" NE2 HIS C 73 " pdb=" OH TYR C 123 " model vdw 2.275 3.120 ... (remaining 42257 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 'C' selection = (chain 'D' and (resid 34 through 290 or resid 317 through 350)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.320 Find NCS groups from input model: 0.070 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 : 0.010 0.124 5561 Z= 0.492 Angle : 0.977 11.986 7600 Z= 0.370 Chirality : 0.035 0.139 855 Planarity : 0.003 0.025 876 Dihedral : 21.460 175.931 2719 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.95 % Allowed : 15.52 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.30 (0.36), residues: 621 helix: 1.82 (0.31), residues: 300 sheet: -0.14 (1.15), residues: 24 loop : 0.03 (0.41), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 92 TYR 0.008 0.001 TYR C 170 PHE 0.009 0.001 PHE C 235 TRP 0.010 0.001 TRP D 259 HIS 0.004 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00989 / 0.49 ( 5561) covalent geometry : angle 0.97685 / 0.37 ( 7600) hydrogen bonds : bond 0.14909 / 10.13 ( 216) hydrogen bonds : angle 4.95853 / 3.65 ( 630) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: C 57 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7606 (tp30) REVERT: C 149 MET cc_start: 0.8047 (tmm) cc_final: 0.7816 (tmm) REVERT: C 333 LYS cc_start: 0.6863 (mmtp) cc_final: 0.6365 (mptt) REVERT: D 72 MET cc_start: 0.7833 (ttm) cc_final: 0.7570 (ttm) REVERT: D 268 GLU cc_start: 0.7759 (tp30) cc_final: 0.7238 (mp0) REVERT: D 303 SER cc_start: 0.8600 (t) cc_final: 0.8021 (m) REVERT: D 329 ASP cc_start: 0.7595 (m-30) cc_final: 0.6597 (p0) outliers start: 15 outliers final: 7 residues processed: 86 average time/residue: 0.0942 time to fit residues: 9.9940 Evaluate side-chains 74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 262 CYS Chi-restraints excluded: chain D residue 315 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [49, 53, 5, 33, 62, 51, 38, 61, 45, 27, 64] chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.0010 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.0060 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 154 ASN C 187 GLN D 96 ASN ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.222818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164682 restraints weight = 5854.747| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.75 r_work: 0.3714 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5561 Z= 0.126 Angle : 0.596 5.118 7600 Z= 0.285 Chirality : 0.037 0.139 855 Planarity : 0.004 0.051 876 Dihedral : 22.433 175.122 1586 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.75 % Allowed : 17.88 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.26 (0.36), residues: 621 helix: 1.59 (0.30), residues: 312 sheet: 0.03 (1.23), residues: 22 loop : 0.17 (0.41), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 92 TYR 0.008 0.001 TYR D 197 PHE 0.008 0.001 PHE D 208 TRP 0.012 0.001 TRP D 259 HIS 0.009 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 5561) covalent geometry : angle 0.59641 / 0.29 ( 7600) hydrogen bonds : bond 0.04289 / 2.81 ( 216) hydrogen bonds : angle 4.24930 / 2.98 ( 630) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.166 Fit side-chains REVERT: C 57 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7411 (tp30) REVERT: C 149 MET cc_start: 0.7992 (tmm) cc_final: 0.7768 (tmm) REVERT: C 198 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7862 (mmt180) REVERT: C 333 LYS cc_start: 0.6867 (mmtp) cc_final: 0.6438 (mptt) REVERT: D 72 MET cc_start: 0.7838 (ttm) cc_final: 0.7615 (ttm) REVERT: D 135 MET cc_start: 0.5583 (tpp) cc_final: 0.5316 (tpp) REVERT: D 268 GLU cc_start: 0.7749 (tp30) cc_final: 0.7117 (mp0) REVERT: D 303 SER cc_start: 0.8583 (t) cc_final: 0.7979 (m) REVERT: D 321 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7043 (pm20) REVERT: D 329 ASP cc_start: 0.7578 (m-30) cc_final: 0.6493 (p0) REVERT: D 336 ARG cc_start: 0.7043 (ptm160) cc_final: 0.6770 (ttm170) outliers start: 14 outliers final: 9 residues processed: 83 average time/residue: 0.1013 time to fit residues: 10.2307 Evaluate side-chains 75 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 313 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [45, 62, 31, 55, 19, 23, 43, 2, 42, 13, 40] chunk 45 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 23 optimal weight: 0.0470 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 96 ASN D 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.223151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.166296 restraints weight = 5819.627| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.70 r_work: 0.3732 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5561 Z= 0.104 Angle : 0.556 4.275 7600 Z= 0.261 Chirality : 0.036 0.139 855 Planarity : 0.003 0.046 876 Dihedral : 22.192 173.823 1577 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.14 % Allowed : 19.45 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.22 (0.35), residues: 621 helix: 1.63 (0.30), residues: 313 sheet: -0.28 (1.18), residues: 22 loop : 0.06 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 336 TYR 0.010 0.001 TYR C 191 PHE 0.007 0.001 PHE C 208 TRP 0.010 0.001 TRP C 259 HIS 0.010 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 5561) covalent geometry : angle 0.55559 / 0.26 ( 7600) hydrogen bonds : bond 0.03526 / 2.30 ( 216) hydrogen bonds : angle 4.07000 / 2.81 ( 630) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.118 Fit side-chains REVERT: C 57 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7471 (tp30) REVERT: C 333 LYS cc_start: 0.6866 (mmtp) cc_final: 0.6423 (mptt) REVERT: D 40 GLU cc_start: 0.7660 (tp30) cc_final: 0.7421 (tm-30) REVERT: D 150 MET cc_start: 0.6774 (tpp) cc_final: 0.6499 (tpt) REVERT: D 268 GLU cc_start: 0.7656 (tp30) cc_final: 0.7054 (mp0) REVERT: D 303 SER cc_start: 0.8593 (t) cc_final: 0.8019 (m) REVERT: D 321 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7064 (pm20) outliers start: 16 outliers final: 12 residues processed: 78 average time/residue: 0.1084 time to fit residues: 10.1437 Evaluate side-chains 76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [32, 11, 13, 52, 48, 8, 44, 33, 54, 57, 53] chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 187 GLN D 96 ASN D 343 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.222578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.165313 restraints weight = 5805.611| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.70 r_work: 0.3722 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5561 Z= 0.114 Angle : 0.562 4.804 7600 Z= 0.265 Chirality : 0.036 0.135 855 Planarity : 0.003 0.031 876 Dihedral : 22.148 175.566 1577 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.34 % Allowed : 19.06 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.08 (0.35), residues: 621 helix: 1.55 (0.30), residues: 313 sheet: -0.46 (1.14), residues: 22 loop : -0.05 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 198 TYR 0.008 0.001 TYR D 342 PHE 0.007 0.001 PHE C 208 TRP 0.012 0.001 TRP D 259 HIS 0.007 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 5561) covalent geometry : angle 0.56181 / 0.27 ( 7600) hydrogen bonds : bond 0.03510 / 2.27 ( 216) hydrogen bonds : angle 4.05768 / 2.79 ( 630) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: C 57 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7100 (tm-30) REVERT: C 83 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6969 (mttt) REVERT: C 333 LYS cc_start: 0.6934 (mmtp) cc_final: 0.6475 (mptt) REVERT: D 96 ASN cc_start: 0.6480 (m-40) cc_final: 0.6212 (t0) REVERT: D 135 MET cc_start: 0.5499 (tpp) cc_final: 0.5230 (tpt) REVERT: D 150 MET cc_start: 0.6817 (tpp) cc_final: 0.6456 (tpt) REVERT: D 268 GLU cc_start: 0.7699 (tp30) cc_final: 0.7103 (mp0) REVERT: D 303 SER cc_start: 0.8624 (t) cc_final: 0.8073 (m) REVERT: D 321 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7029 (pm20) REVERT: D 329 ASP cc_start: 0.7549 (m-30) cc_final: 0.6448 (p0) outliers start: 17 outliers final: 13 residues processed: 80 average time/residue: 0.1002 time to fit residues: 9.8315 Evaluate side-chains 82 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [47, 20, 18, 48, 4, 57, 15, 58, 41, 7, 21] chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 48 optimal weight: 0.0870 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 0.0470 chunk 15 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.0010 overall best weight: 0.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 187 GLN D 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.224604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.167471 restraints weight = 5883.393| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.74 r_work: 0.3747 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5561 Z= 0.093 Angle : 0.543 3.840 7600 Z= 0.255 Chirality : 0.035 0.140 855 Planarity : 0.003 0.030 876 Dihedral : 21.970 174.509 1577 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.36 % Allowed : 20.24 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.13 (0.35), residues: 621 helix: 1.64 (0.30), residues: 313 sheet: -0.56 (1.14), residues: 22 loop : -0.07 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 336 TYR 0.006 0.001 TYR D 197 PHE 0.006 0.001 PHE C 68 TRP 0.012 0.001 TRP D 120 HIS 0.004 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 ( 5561) covalent geometry : angle 0.54311 / 0.26 ( 7600) hydrogen bonds : bond 0.03228 / 2.12 ( 216) hydrogen bonds : angle 3.94286 / 2.70 ( 630) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.180 Fit side-chains REVERT: C 57 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7120 (tm-30) REVERT: C 333 LYS cc_start: 0.7032 (mmtp) cc_final: 0.6545 (mptt) REVERT: D 96 ASN cc_start: 0.6513 (m-40) cc_final: 0.6272 (t0) REVERT: D 135 MET cc_start: 0.5462 (tpp) cc_final: 0.5209 (tpt) REVERT: D 150 MET cc_start: 0.6832 (tpp) cc_final: 0.6566 (tpt) REVERT: D 268 GLU cc_start: 0.7677 (tp30) cc_final: 0.7144 (mp0) REVERT: D 303 SER cc_start: 0.8570 (t) cc_final: 0.8041 (m) REVERT: D 321 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7131 (pm20) REVERT: D 329 ASP cc_start: 0.7572 (m-30) cc_final: 0.6418 (p0) outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.0922 time to fit residues: 9.1654 Evaluate side-chains 77 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [37, 36, 31, 18, 40, 26, 2, 17, 28, 42, 38] chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 343 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.221236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.166897 restraints weight = 5660.510| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.51 r_work: 0.3744 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5561 Z= 0.112 Angle : 0.560 6.210 7600 Z= 0.261 Chirality : 0.036 0.139 855 Planarity : 0.003 0.030 876 Dihedral : 21.870 172.478 1577 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.36 % Allowed : 22.00 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.02 (0.35), residues: 621 helix: 1.54 (0.30), residues: 313 sheet: -0.62 (1.13), residues: 22 loop : -0.11 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 56 TYR 0.007 0.001 TYR C 170 PHE 0.006 0.001 PHE C 208 TRP 0.012 0.001 TRP C 259 HIS 0.005 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 5561) covalent geometry : angle 0.56044 / 0.26 ( 7600) hydrogen bonds : bond 0.03265 / 2.12 ( 216) hydrogen bonds : angle 3.98041 / 2.72 ( 630) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.188 Fit side-chains REVERT: C 57 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7100 (tm-30) REVERT: C 333 LYS cc_start: 0.7019 (mmtp) cc_final: 0.6586 (mptt) REVERT: D 135 MET cc_start: 0.5451 (tpp) cc_final: 0.5249 (tpt) REVERT: D 268 GLU cc_start: 0.7740 (tp30) cc_final: 0.7101 (mp0) REVERT: D 303 SER cc_start: 0.8615 (t) cc_final: 0.8096 (m) REVERT: D 329 ASP cc_start: 0.7554 (m-30) cc_final: 0.6400 (p0) outliers start: 12 outliers final: 11 residues processed: 77 average time/residue: 0.0906 time to fit residues: 8.8069 Evaluate side-chains 77 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [48, 35, 6, 32, 11, 41, 2, 34, 55, 16, 26] chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 2 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 96 ASN D 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.222471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.165311 restraints weight = 5856.419| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.72 r_work: 0.3725 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5561 Z= 0.113 Angle : 0.581 6.296 7600 Z= 0.272 Chirality : 0.036 0.139 855 Planarity : 0.003 0.029 876 Dihedral : 21.756 171.732 1577 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.75 % Allowed : 21.61 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.93 (0.35), residues: 621 helix: 1.49 (0.30), residues: 313 sheet: -0.61 (1.13), residues: 22 loop : -0.20 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 56 TYR 0.008 0.001 TYR C 170 PHE 0.006 0.001 PHE C 208 TRP 0.011 0.001 TRP C 259 HIS 0.008 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 5561) covalent geometry : angle 0.58113 / 0.27 ( 7600) hydrogen bonds : bond 0.03283 / 2.13 ( 216) hydrogen bonds : angle 3.99019 / 2.73 ( 630) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.169 Fit side-chains REVERT: C 57 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7106 (tm-30) REVERT: C 92 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7500 (mmm-85) REVERT: C 333 LYS cc_start: 0.7030 (mmtp) cc_final: 0.6596 (mptt) REVERT: D 268 GLU cc_start: 0.7766 (tp30) cc_final: 0.7085 (mp0) REVERT: D 303 SER cc_start: 0.8591 (t) cc_final: 0.8096 (m) REVERT: D 321 GLU cc_start: 0.5916 (pm20) cc_final: 0.5645 (pm20) outliers start: 14 outliers final: 13 residues processed: 73 average time/residue: 0.0938 time to fit residues: 8.4358 Evaluate side-chains 76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [2, 23, 7, 44, 43, 3, 25, 41, 8, 56, 63] chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.0170 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 187 GLN D 96 ASN D 343 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.223684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.166715 restraints weight = 5821.801| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.72 r_work: 0.3741 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5561 Z= 0.096 Angle : 0.573 6.466 7600 Z= 0.266 Chirality : 0.036 0.135 855 Planarity : 0.003 0.031 876 Dihedral : 21.585 171.659 1577 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.55 % Allowed : 21.61 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.99 (0.35), residues: 621 helix: 1.58 (0.30), residues: 313 sheet: -0.57 (1.13), residues: 22 loop : -0.22 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 56 TYR 0.012 0.001 TYR D 342 PHE 0.006 0.001 PHE C 68 TRP 0.011 0.001 TRP D 259 HIS 0.006 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 5561) covalent geometry : angle 0.57279 / 0.27 ( 7600) hydrogen bonds : bond 0.03136 / 2.05 ( 216) hydrogen bonds : angle 3.96857 / 2.73 ( 630) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.118 Fit side-chains REVERT: C 57 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7094 (tm-30) REVERT: C 92 ARG cc_start: 0.7815 (mmm-85) cc_final: 0.7494 (mmm-85) REVERT: C 333 LYS cc_start: 0.7039 (mmtp) cc_final: 0.6587 (mptt) REVERT: D 268 GLU cc_start: 0.7749 (tp30) cc_final: 0.7037 (mp0) REVERT: D 303 SER cc_start: 0.8577 (t) cc_final: 0.8075 (m) REVERT: D 321 GLU cc_start: 0.5913 (pm20) cc_final: 0.5709 (pm20) outliers start: 13 outliers final: 12 residues processed: 75 average time/residue: 0.0891 time to fit residues: 8.2944 Evaluate side-chains 76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [42, 58, 48, 20, 12, 31, 13, 36, 11, 49, 23] chunk 42 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 20 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 23 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 343 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.223403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.166300 restraints weight = 5819.990| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.71 r_work: 0.3738 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5561 Z= 0.104 Angle : 0.572 5.162 7600 Z= 0.269 Chirality : 0.036 0.137 855 Planarity : 0.003 0.033 876 Dihedral : 21.474 171.423 1577 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.36 % Allowed : 22.00 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.86 (0.35), residues: 621 helix: 1.44 (0.30), residues: 314 sheet: -0.58 (1.13), residues: 22 loop : -0.25 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 56 TYR 0.007 0.001 TYR D 197 PHE 0.006 0.001 PHE C 68 TRP 0.013 0.001 TRP C 259 HIS 0.003 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 5561) covalent geometry : angle 0.57199 / 0.27 ( 7600) hydrogen bonds : bond 0.03160 / 2.06 ( 216) hydrogen bonds : angle 4.04207 / 2.79 ( 630) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.184 Fit side-chains REVERT: C 57 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7087 (tm-30) REVERT: C 92 ARG cc_start: 0.7829 (mmm-85) cc_final: 0.7558 (mmm-85) REVERT: C 109 ARG cc_start: 0.7100 (mmt180) cc_final: 0.6831 (mmt180) REVERT: C 333 LYS cc_start: 0.7067 (mmtp) cc_final: 0.6613 (mptt) REVERT: D 268 GLU cc_start: 0.7759 (tp30) cc_final: 0.7161 (mp0) REVERT: D 303 SER cc_start: 0.8581 (t) cc_final: 0.8081 (m) outliers start: 12 outliers final: 12 residues processed: 71 average time/residue: 0.0990 time to fit residues: 8.7075 Evaluate side-chains 73 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [48, 56, 33, 52, 42, 31, 13, 50, 23, 41, 11] chunk 48 optimal weight: 0.0970 chunk 56 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 343 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.224114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.167176 restraints weight = 5821.574| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.70 r_work: 0.3748 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5561 Z= 0.097 Angle : 0.570 5.358 7600 Z= 0.267 Chirality : 0.035 0.134 855 Planarity : 0.003 0.033 876 Dihedral : 21.432 171.360 1577 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.75 % Allowed : 21.81 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.87 (0.35), residues: 621 helix: 1.46 (0.30), residues: 314 sheet: -0.61 (1.12), residues: 22 loop : -0.26 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 56 TYR 0.011 0.001 TYR D 342 PHE 0.006 0.001 PHE C 68 TRP 0.013 0.001 TRP C 259 HIS 0.011 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 5561) covalent geometry : angle 0.56986 / 0.27 ( 7600) hydrogen bonds : bond 0.03091 / 2.04 ( 216) hydrogen bonds : angle 4.00745 / 2.76 ( 630) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: C 57 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7091 (tm-30) REVERT: C 333 LYS cc_start: 0.7102 (mmtp) cc_final: 0.6628 (mptt) REVERT: D 268 GLU cc_start: 0.7791 (tp30) cc_final: 0.7148 (mp0) REVERT: D 303 SER cc_start: 0.8523 (t) cc_final: 0.8032 (m) outliers start: 14 outliers final: 13 residues processed: 73 average time/residue: 0.0961 time to fit residues: 8.7061 Evaluate side-chains 76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [17, 60, 18, 58, 1, 20, 53, 56, 55, 63, 38] chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 53 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 overall best weight: 1.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 343 HIS E 300 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.220338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.163159 restraints weight = 5925.907| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.71 r_work: 0.3711 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5561 Z= 0.177 Angle : 0.620 4.887 7600 Z= 0.295 Chirality : 0.038 0.148 855 Planarity : 0.003 0.034 876 Dihedral : 21.462 169.710 1577 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.95 % Allowed : 21.81 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.62 (0.34), residues: 621 helix: 1.21 (0.29), residues: 314 sheet: -0.74 (1.12), residues: 22 loop : -0.33 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 56 TYR 0.012 0.002 TYR D 342 PHE 0.010 0.002 PHE D 189 TRP 0.014 0.002 TRP C 259 HIS 0.004 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 5561) covalent geometry : angle 0.61981 / 0.30 ( 7600) hydrogen bonds : bond 0.03677 / 2.43 ( 216) hydrogen bonds : angle 4.26489 / 2.96 ( 630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1458.60 seconds wall clock time: 25 minutes 44.42 seconds (1544.42 seconds total)