Starting phenix.real_space_refine on Wed Sep 17 05:34:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqi_21351/09_2025/6vqi_21351.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqi_21351/09_2025/6vqi_21351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vqi_21351/09_2025/6vqi_21351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqi_21351/09_2025/6vqi_21351.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vqi_21351/09_2025/6vqi_21351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqi_21351/09_2025/6vqi_21351.map" } resolution = 4.3 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= 0.055 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: 3 Type Number sf(0) Gaussians C 3154 2.51 5 N 1062 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5278 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 1790 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 325} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 350} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1192 Unresolved non-hydrogen angles: 1522 Unresolved non-hydrogen dihedrals: 998 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'GLU:plan': 25, 'PHE:plan': 14, 'TRP:plan': 6, 'GLN:plan1': 16, 'HIS:plan': 6, 'ASN:plan1': 22, 'ASP:plan': 24, 'TYR:plan': 15, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 645 Chain: "I" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 319 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 132 Chain: "J" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 319 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 132 Chain: "K" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 319 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 132 Chain: "M" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 332 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 13, 'GLU:plan': 9, 'ARG:plan': 8, 'ASP:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 147 Chain: "N" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 332 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 13, 'GLU:plan': 9, 'ARG:plan': 8, 'ASP:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 147 Chain: "O" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 332 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 13, 'GLU:plan': 9, 'ARG:plan': 8, 'ASP:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 147 Chain: "a" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 1535 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 283} Link IDs: {'PTRANS': 13, 'TRANS': 295} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1046 Unresolved non-hydrogen angles: 1326 Unresolved non-hydrogen dihedrals: 856 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 16, 'PHE:plan': 18, 'GLU:plan': 31, 'TYR:plan': 4, 'ARG:plan': 26, 'ASP:plan': 15, 'ASN:plan1': 20, 'TRP:plan': 3, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 606 Time building chain proxies: 1.82, per 1000 atoms: 0.34 Number of scatterers: 5278 At special positions: 0 Unit cell: (147.34, 147.34, 139.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1062 8.00 N 1062 7.00 C 3154 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: 0.58 Conformation dependent library (CDL) restraints added in 319.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 6 sheets defined 72.7% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'G' and resid 15 through 20 removed outlier: 3.575A pdb=" N GLU G 20 " --> pdb=" O GLN G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 80 Processing helix chain 'G' and resid 97 through 104 Processing helix chain 'G' and resid 117 through 157 Processing helix chain 'G' and resid 171 through 175 Processing helix chain 'G' and resid 193 through 201 Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 254 through 311 Proline residue: G 278 - end of helix removed outlier: 3.628A pdb=" N ARG G 281 " --> pdb=" O GLY G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 344 removed outlier: 5.308A pdb=" N HIS G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU G 342 " --> pdb=" O LEU G 338 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP G 343 " --> pdb=" O TYR G 339 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 65 Processing helix chain 'J' and resid 4 through 65 Processing helix chain 'K' and resid 4 through 65 Processing helix chain 'M' and resid 4 through 69 Processing helix chain 'N' and resid 4 through 69 Processing helix chain 'O' and resid 4 through 69 Processing helix chain 'a' and resid 19 through 33 removed outlier: 3.635A pdb=" N CYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 50 Processing helix chain 'a' and resid 51 through 75 removed outlier: 3.543A pdb=" N GLU a 71 " --> pdb=" O PHE a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 88 Processing helix chain 'a' and resid 93 through 132 Processing helix chain 'a' and resid 179 through 191 removed outlier: 4.152A pdb=" N ARG a 185 " --> pdb=" O PRO a 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 226 through 240 Processing helix chain 'a' and resid 251 through 309 removed outlier: 3.588A pdb=" N LYS a 255 " --> pdb=" O PRO a 251 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN a 289 " --> pdb=" O ALA a 285 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL a 292 " --> pdb=" O LYS a 288 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE a 295 " --> pdb=" O ARG a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 329 through 344 Processing sheet with id=AA1, first strand: chain 'G' and resid 34 through 37 removed outlier: 3.528A pdb=" N VAL G 34 " --> pdb=" O GLN G 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 214 through 218 removed outlier: 5.773A pdb=" N VAL G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 36 through 37 removed outlier: 3.759A pdb=" N ILE a 320 " --> pdb=" O ASN a 311 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN a 311 " --> pdb=" O ILE a 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 36 through 37 removed outlier: 3.530A pdb=" N PHE a 16 " --> pdb=" O ILE a 351 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE a 351 " --> pdb=" O PHE a 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 197 through 202 removed outlier: 4.411A pdb=" N LYS a 217 " --> pdb=" O ILE a 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 207 through 208 removed outlier: 3.692A pdb=" N ASP a 213 " --> pdb=" O ASP a 208 " (cutoff:3.500A) 705 hydrogen bonds defined for protein. 2085 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: 0.99 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 1062 1.28 - 1.35: 1049 1.35 - 1.41: 3 1.41 - 1.48: 1036 1.48 - 1.55: 2118 Bond restraints: 5268 Sorted by residual: bond pdb=" N VAL a 210 " pdb=" CA VAL a 210 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.74e+00 bond pdb=" N ILE J 64 " pdb=" CA ILE J 64 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.33e+00 bond pdb=" N ILE K 64 " pdb=" CA ILE K 64 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.12e+00 bond pdb=" N ASP a 213 " pdb=" CA ASP a 213 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.98e+00 bond pdb=" N LYS K 60 " pdb=" CA LYS K 60 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.78e+00 ... (remaining 5263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 6763 2.12 - 4.24: 526 4.24 - 6.36: 43 6.36 - 8.48: 6 8.48 - 10.61: 2 Bond angle restraints: 7340 Sorted by residual: angle pdb=" N CYS a 247 " pdb=" CA CYS a 247 " pdb=" C CYS a 247 " ideal model delta sigma weight residual 108.27 97.66 10.61 2.25e+00 1.98e-01 2.22e+01 angle pdb=" N GLN a 252 " pdb=" CA GLN a 252 " pdb=" C GLN a 252 " ideal model delta sigma weight residual 111.71 106.58 5.13 1.15e+00 7.56e-01 1.99e+01 angle pdb=" C PRO a 246 " pdb=" N CYS a 247 " pdb=" CA CYS a 247 " ideal model delta sigma weight residual 123.30 116.96 6.34 1.44e+00 4.82e-01 1.94e+01 angle pdb=" N LEU a 244 " pdb=" CA LEU a 244 " pdb=" C LEU a 244 " ideal model delta sigma weight residual 107.80 115.38 -7.58 1.73e+00 3.34e-01 1.92e+01 angle pdb=" N PRO a 248 " pdb=" CA PRO a 248 " pdb=" C PRO a 248 " ideal model delta sigma weight residual 111.68 118.99 -7.31 1.67e+00 3.59e-01 1.92e+01 ... (remaining 7335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.66: 2804 3.66 - 7.32: 248 7.32 - 10.98: 41 10.98 - 14.64: 17 14.64 - 18.31: 2 Dihedral angle restraints: 3112 sinusoidal: 0 harmonic: 3112 Sorted by residual: dihedral pdb=" CA LYS G 21 " pdb=" C LYS G 21 " pdb=" N LEU G 22 " pdb=" CA LEU G 22 " ideal model delta harmonic sigma weight residual 180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA THR G 27 " pdb=" C THR G 27 " pdb=" N LYS G 28 " pdb=" CA LYS G 28 " ideal model delta harmonic sigma weight residual -180.00 -163.66 -16.34 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA VAL a 323 " pdb=" C VAL a 323 " pdb=" N TRP a 324 " pdb=" CA TRP a 324 " ideal model delta harmonic sigma weight residual 180.00 166.36 13.64 0 5.00e+00 4.00e-02 7.44e+00 ... (remaining 3109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 795 0.045 - 0.090: 158 0.090 - 0.136: 56 0.136 - 0.181: 14 0.181 - 0.226: 7 Chirality restraints: 1030 Sorted by residual: chirality pdb=" CA PRO a 248 " pdb=" N PRO a 248 " pdb=" C PRO a 248 " pdb=" CB PRO a 248 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE J 64 " pdb=" N ILE J 64 " pdb=" C ILE J 64 " pdb=" CB ILE J 64 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA VAL a 210 " pdb=" N VAL a 210 " pdb=" C VAL a 210 " pdb=" CB VAL a 210 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1027 not shown) Planarity restraints: 1052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP G 236 " -0.022 2.00e-02 2.50e+03 4.40e-02 1.94e+01 pdb=" C ASP G 236 " 0.076 2.00e-02 2.50e+03 pdb=" O ASP G 236 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE G 237 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS a 103 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" C LYS a 103 " -0.069 2.00e-02 2.50e+03 pdb=" O LYS a 103 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE a 104 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 196 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ASP G 196 " -0.062 2.00e-02 2.50e+03 pdb=" O ASP G 196 " 0.023 2.00e-02 2.50e+03 pdb=" N TRP G 197 " 0.021 2.00e-02 2.50e+03 ... (remaining 1049 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 2363 2.88 - 3.38: 6152 3.38 - 3.89: 8135 3.89 - 4.39: 8344 4.39 - 4.90: 12331 Nonbonded interactions: 37325 Sorted by model distance: nonbonded pdb=" O ILE a 175 " pdb=" N SER a 218 " model vdw 2.370 3.120 nonbonded pdb=" O HIS G 23 " pdb=" N THR G 27 " model vdw 2.371 3.120 nonbonded pdb=" O GLN G 275 " pdb=" N LEU G 279 " model vdw 2.386 3.120 nonbonded pdb=" N PHE a 170 " pdb=" O ILE a 221 " model vdw 2.411 3.120 nonbonded pdb=" O SER G 160 " pdb=" N ARG G 164 " model vdw 2.425 3.120 ... (remaining 37320 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 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5268 Z= 0.380 Angle : 1.142 10.606 7340 Z= 0.870 Chirality : 0.048 0.226 1030 Planarity : 0.008 0.044 1052 Dihedral : 3.901 18.306 1052 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.48 % Allowed : 1.34 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 2.16 (0.23), residues: 1042 helix: 1.98 (0.16), residues: 740 sheet: 0.89 (0.55), residues: 67 loop : -0.07 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 75 PHE 0.000 0.000 PHE G 4 TRP 0.000 0.000 TRP G 5 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 5268) covalent geometry : angle 1.14197 ( 7340) hydrogen bonds : bond 0.10747 ( 703) hydrogen bonds : angle 4.93660 ( 2085) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.259 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0231 time to fit residues: 1.4524 Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 30.0000 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.062941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.048765 restraints weight = 60472.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.048667 restraints weight = 49897.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.048770 restraints weight = 43654.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.048851 restraints weight = 41461.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.048899 restraints weight = 39543.456| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5268 Z= 0.241 Angle : 0.494 6.434 7340 Z= 0.342 Chirality : 0.036 0.124 1030 Planarity : 0.003 0.016 1052 Dihedral : 4.635 21.770 1052 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 3.38 (0.24), residues: 1042 helix: 2.99 (0.16), residues: 754 sheet: 1.44 (0.58), residues: 71 loop : -0.36 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 75 PHE 0.000 0.000 PHE G 4 TRP 0.000 0.000 TRP G 5 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5268) covalent geometry : angle 0.49449 ( 7340) hydrogen bonds : bond 0.05204 ( 703) hydrogen bonds : angle 4.52130 ( 2085) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.218 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0247 time to fit residues: 1.6319 Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 5.9990 chunk 31 optimal weight: 30.0000 chunk 75 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 88 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.062073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.048261 restraints weight = 60995.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.048408 restraints weight = 54173.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.048593 restraints weight = 44535.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.048647 restraints weight = 42583.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.048706 restraints weight = 40158.475| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5268 Z= 0.279 Angle : 0.521 5.900 7340 Z= 0.368 Chirality : 0.036 0.147 1030 Planarity : 0.003 0.012 1052 Dihedral : 4.750 27.159 1052 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.50 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 2.81 (0.25), residues: 1042 helix: 2.86 (0.17), residues: 736 sheet: 0.60 (0.59), residues: 63 loop : -1.08 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 75 PHE 0.000 0.000 PHE G 4 TRP 0.000 0.000 TRP G 5 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5268) covalent geometry : angle 0.52148 ( 7340) hydrogen bonds : bond 0.05711 ( 703) hydrogen bonds : angle 4.94151 ( 2085) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.258 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0262 time to fit residues: 1.7467 Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 30.0000 chunk 70 optimal weight: 10.0000 chunk 60 optimal weight: 40.0000 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 79 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.061966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.047135 restraints weight = 59790.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.047329 restraints weight = 49942.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.047512 restraints weight = 40691.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.047608 restraints weight = 37935.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.047785 restraints weight = 36092.317| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5268 Z= 0.194 Angle : 0.427 5.241 7340 Z= 0.296 Chirality : 0.035 0.140 1030 Planarity : 0.002 0.010 1052 Dihedral : 4.250 21.853 1052 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 3.25 (0.25), residues: 1042 helix: 3.27 (0.16), residues: 733 sheet: 0.13 (0.54), residues: 72 loop : -1.03 (0.45), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 75 PHE 0.000 0.000 PHE G 4 TRP 0.000 0.000 TRP G 5 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 5268) covalent geometry : angle 0.42703 ( 7340) hydrogen bonds : bond 0.04611 ( 703) hydrogen bonds : angle 4.38035 ( 2085) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0251 time to fit residues: 1.6274 Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 88 optimal weight: 40.0000 chunk 79 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 chunk 84 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 23 optimal weight: 50.0000 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.060717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.046745 restraints weight = 63217.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.046605 restraints weight = 51857.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.046739 restraints weight = 43981.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.046886 restraints weight = 41921.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.046978 restraints weight = 37846.780| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5268 Z= 0.242 Angle : 0.475 5.229 7340 Z= 0.334 Chirality : 0.035 0.133 1030 Planarity : 0.003 0.012 1052 Dihedral : 4.704 23.741 1052 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 2.47 (0.25), residues: 1042 helix: 2.75 (0.17), residues: 736 sheet: -0.53 (0.54), residues: 74 loop : -1.46 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 75 PHE 0.000 0.000 PHE G 4 TRP 0.000 0.000 TRP G 5 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5268) covalent geometry : angle 0.47483 ( 7340) hydrogen bonds : bond 0.05227 ( 703) hydrogen bonds : angle 4.88764 ( 2085) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.218 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0233 time to fit residues: 1.5993 Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 83 optimal weight: 8.9990 chunk 40 optimal weight: 50.0000 chunk 13 optimal weight: 30.0000 chunk 94 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 50.0000 chunk 33 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 50.0000 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.059472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.044603 restraints weight = 61591.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.045185 restraints weight = 45376.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.045315 restraints weight = 32468.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.045514 restraints weight = 31010.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.045683 restraints weight = 28284.923| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5268 Z= 0.335 Angle : 0.580 5.786 7340 Z= 0.412 Chirality : 0.037 0.132 1030 Planarity : 0.004 0.014 1052 Dihedral : 5.429 27.490 1052 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.14 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.65 (0.26), residues: 1042 helix: 1.41 (0.18), residues: 734 sheet: -1.32 (0.56), residues: 74 loop : -2.11 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 75 PHE 0.000 0.000 PHE G 4 TRP 0.000 0.000 TRP G 5 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 5268) covalent geometry : angle 0.57972 ( 7340) hydrogen bonds : bond 0.06332 ( 703) hydrogen bonds : angle 5.72313 ( 2085) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0238 time to fit residues: 1.5648 Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 13 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.060631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.046934 restraints weight = 62815.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.046725 restraints weight = 51044.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.046895 restraints weight = 43631.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.047023 restraints weight = 41114.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.047084 restraints weight = 37150.408| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5268 Z= 0.199 Angle : 0.422 3.662 7340 Z= 0.296 Chirality : 0.035 0.125 1030 Planarity : 0.002 0.010 1052 Dihedral : 4.508 21.706 1052 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.37 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 2.09 (0.26), residues: 1042 helix: 2.58 (0.17), residues: 730 sheet: -1.30 (0.57), residues: 74 loop : -1.69 (0.46), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 75 PHE 0.000 0.000 PHE G 4 TRP 0.000 0.000 TRP G 5 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 5268) covalent geometry : angle 0.42231 ( 7340) hydrogen bonds : bond 0.04693 ( 703) hydrogen bonds : angle 4.64385 ( 2085) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.197 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0238 time to fit residues: 1.5511 Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 32 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 18 optimal weight: 50.0000 chunk 56 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 20 optimal weight: 50.0000 chunk 44 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 88 optimal weight: 50.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.060073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.044434 restraints weight = 62950.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.045140 restraints weight = 45069.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.045611 restraints weight = 36040.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.045867 restraints weight = 30888.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.046116 restraints weight = 27670.360| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5268 Z= 0.254 Angle : 0.481 4.183 7340 Z= 0.341 Chirality : 0.035 0.124 1030 Planarity : 0.003 0.012 1052 Dihedral : 4.821 23.798 1052 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.20 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.57 (0.27), residues: 1042 helix: 2.20 (0.17), residues: 729 sheet: -1.62 (0.57), residues: 74 loop : -1.83 (0.47), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 75 PHE 0.000 0.000 PHE G 4 TRP 0.000 0.000 TRP G 5 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5268) covalent geometry : angle 0.48093 ( 7340) hydrogen bonds : bond 0.05291 ( 703) hydrogen bonds : angle 5.03930 ( 2085) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.212 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0245 time to fit residues: 1.6089 Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 6.9990 chunk 89 optimal weight: 50.0000 chunk 28 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 99 optimal weight: 40.0000 chunk 15 optimal weight: 50.0000 chunk 87 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 94 optimal weight: 30.0000 chunk 82 optimal weight: 6.9990 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.059765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.044252 restraints weight = 62877.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.044961 restraints weight = 44733.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.045430 restraints weight = 35680.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.045838 restraints weight = 29310.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.046017 restraints weight = 26796.491| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5268 Z= 0.282 Angle : 0.509 4.280 7340 Z= 0.363 Chirality : 0.036 0.127 1030 Planarity : 0.003 0.013 1052 Dihedral : 4.937 24.908 1052 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.72 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.01 (0.26), residues: 1042 helix: 1.81 (0.18), residues: 734 sheet: -1.94 (0.58), residues: 74 loop : -2.18 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 75 PHE 0.000 0.000 PHE G 4 TRP 0.000 0.000 TRP G 5 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 5268) covalent geometry : angle 0.50890 ( 7340) hydrogen bonds : bond 0.05514 ( 703) hydrogen bonds : angle 5.23821 ( 2085) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.212 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0225 time to fit residues: 1.5363 Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 82 optimal weight: 9.9990 chunk 89 optimal weight: 50.0000 chunk 10 optimal weight: 0.5980 chunk 72 optimal weight: 40.0000 chunk 51 optimal weight: 50.0000 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 59 optimal weight: 30.0000 chunk 74 optimal weight: 20.0000 overall best weight: 6.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.060414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.046913 restraints weight = 63283.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.046906 restraints weight = 49710.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.046952 restraints weight = 43684.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.047045 restraints weight = 41587.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.047145 restraints weight = 38779.979| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5268 Z= 0.207 Angle : 0.432 3.590 7340 Z= 0.304 Chirality : 0.035 0.123 1030 Planarity : 0.002 0.010 1052 Dihedral : 4.560 21.761 1052 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.81 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.80 (0.27), residues: 1042 helix: 2.46 (0.17), residues: 730 sheet: -1.93 (0.59), residues: 74 loop : -1.93 (0.46), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 75 PHE 0.000 0.000 PHE G 4 TRP 0.000 0.000 TRP G 5 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 5268) covalent geometry : angle 0.43245 ( 7340) hydrogen bonds : bond 0.04759 ( 703) hydrogen bonds : angle 4.68690 ( 2085) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.208 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0240 time to fit residues: 1.5861 Evaluate side-chains 29 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 69 optimal weight: 50.0000 chunk 86 optimal weight: 30.0000 chunk 7 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.061850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.049875 restraints weight = 60962.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.049581 restraints weight = 45538.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.049879 restraints weight = 40577.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.049762 restraints weight = 35393.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.049880 restraints weight = 32682.499| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5268 Z= 0.252 Angle : 0.477 4.087 7340 Z= 0.339 Chirality : 0.036 0.127 1030 Planarity : 0.003 0.012 1052 Dihedral : 4.795 23.881 1052 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.16 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.23 (0.26), residues: 1042 helix: 2.07 (0.18), residues: 735 sheet: -1.94 (0.58), residues: 76 loop : -2.45 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 75 PHE 0.000 0.000 PHE G 4 TRP 0.000 0.000 TRP G 5 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 5268) covalent geometry : angle 0.47708 ( 7340) hydrogen bonds : bond 0.05281 ( 703) hydrogen bonds : angle 5.03832 ( 2085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1317.64 seconds wall clock time: 23 minutes 9.15 seconds (1389.15 seconds total)