Starting phenix.real_space_refine on Tue Feb 11 10:38:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqi_21351/02_2025/6vqi_21351.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqi_21351/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vqi_21351/02_2025/6vqi_21351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqi_21351/02_2025/6vqi_21351.map" model { file = "/net/cci-nas-00/data/ceres_data/6vqi_21351/02_2025/6vqi_21351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqi_21351/02_2025/6vqi_21351.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.055 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 16, 'ARG:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 6, 'HIS:plan': 6, 'PHE:plan': 14, 'GLU:plan': 25, 'ASP:plan': 24} 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: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASP:plan': 3} 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: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASP:plan': 3} 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: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASP:plan': 3} 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, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} 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, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} 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, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} 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, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 20, 'TRP:plan': 3, 'ASP:plan': 15, 'PHE:plan': 18, 'GLU:plan': 31, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 606 Time building chain proxies: 4.65, per 1000 atoms: 0.88 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: 1.55 Conformation dependent library (CDL) restraints added in 972.4 milliseconds 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: 0.42 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: 1.43 Time building geometry restraints manager: 1.76 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: 2.000 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.010 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.330 ------------------------------------------------------------------------------- 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= 0.355 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.000 0.000 TRP G 5 PHE 0.000 0.000 PHE G 4 TYR 0.000 0.000 TYR G 75 *********************** 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 : 0.617 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0514 time to fit residues: 3.5956 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 : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 50.0000 chunk 26 optimal weight: 50.0000 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 50.0000 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.063705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.049484 restraints weight = 61282.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.049338 restraints weight = 52652.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.049486 restraints weight = 46914.854| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5268 Z= 0.176 Angle : 0.429 5.341 7340 Z= 0.293 Chirality : 0.035 0.125 1030 Planarity : 0.003 0.014 1052 Dihedral : 4.040 19.406 1052 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.32 (0.24), residues: 1042 helix: 3.80 (0.15), residues: 751 sheet: 1.76 (0.58), residues: 65 loop : -0.40 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP G 5 PHE 0.000 0.000 PHE G 4 TYR 0.000 0.000 TYR G 75 *********************** 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 : 0.668 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0508 time to fit residues: 3.6849 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 : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 23 optimal weight: 50.0000 chunk 50 optimal weight: 50.0000 chunk 65 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 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 = 0.3645 r_free = 0.3645 target = 0.063761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.050049 restraints weight = 58209.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.049499 restraints weight = 51459.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.049879 restraints weight = 45005.506| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 5268 Z= 0.235 Angle : 0.479 6.105 7340 Z= 0.335 Chirality : 0.035 0.145 1030 Planarity : 0.003 0.011 1052 Dihedral : 4.440 25.705 1052 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.24), residues: 1042 helix: 3.37 (0.16), residues: 742 sheet: 1.13 (0.61), residues: 63 loop : -0.93 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP G 5 PHE 0.000 0.000 PHE G 4 TYR 0.000 0.000 TYR G 75 *********************** 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 : 0.526 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0484 time to fit residues: 3.4315 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 : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 7.9990 chunk 44 optimal weight: 30.0000 chunk 66 optimal weight: 40.0000 chunk 46 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 87 optimal weight: 40.0000 chunk 59 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.062974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.049145 restraints weight = 60577.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.049066 restraints weight = 49712.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.049253 restraints weight = 43546.380| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 5268 Z= 0.161 Angle : 0.391 4.958 7340 Z= 0.269 Chirality : 0.035 0.139 1030 Planarity : 0.002 0.009 1052 Dihedral : 3.908 20.457 1052 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.25), residues: 1042 helix: 3.68 (0.16), residues: 753 sheet: 1.04 (0.59), residues: 71 loop : -0.63 (0.47), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP G 5 PHE 0.000 0.000 PHE G 4 TYR 0.000 0.000 TYR G 75 *********************** 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 : 0.665 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0482 time to fit residues: 3.4961 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 : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 50.0000 chunk 92 optimal weight: 9.9990 chunk 28 optimal weight: 30.0000 chunk 23 optimal weight: 50.0000 chunk 39 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 56 optimal weight: 40.0000 chunk 65 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 72 optimal weight: 30.0000 chunk 71 optimal weight: 9.9990 overall best weight: 11.9994 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.060167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.045980 restraints weight = 60548.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.046201 restraints weight = 48927.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.046210 restraints weight = 38474.280| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5268 Z= 0.349 Angle : 0.613 6.849 7340 Z= 0.438 Chirality : 0.037 0.142 1030 Planarity : 0.004 0.016 1052 Dihedral : 5.574 30.095 1052 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.69 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 : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1042 helix: 1.55 (0.17), residues: 743 sheet: -0.62 (0.53), residues: 72 loop : -1.63 (0.44), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP G 5 PHE 0.000 0.000 PHE G 4 TYR 0.000 0.000 TYR G 75 *********************** 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 : 0.647 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0466 time to fit residues: 3.4115 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 : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 40 optimal weight: 30.0000 chunk 22 optimal weight: 50.0000 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.060672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.046414 restraints weight = 61989.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.046587 restraints weight = 48607.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.046694 restraints weight = 39634.824| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5268 Z= 0.217 Angle : 0.462 4.738 7340 Z= 0.324 Chirality : 0.035 0.136 1030 Planarity : 0.003 0.011 1052 Dihedral : 4.621 23.344 1052 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.26), residues: 1042 helix: 2.40 (0.17), residues: 736 sheet: -1.07 (0.50), residues: 74 loop : -1.59 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP G 5 PHE 0.000 0.000 PHE G 4 TYR 0.000 0.000 TYR G 75 *********************** 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 : 0.633 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0482 time to fit residues: 3.5285 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 : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 30.0000 chunk 48 optimal weight: 50.0000 chunk 79 optimal weight: 30.0000 chunk 73 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 21 optimal weight: 40.0000 chunk 1 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 23 optimal weight: 50.0000 chunk 35 optimal weight: 10.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.058835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.043738 restraints weight = 59648.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.044591 restraints weight = 39582.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.045143 restraints weight = 30098.659| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 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 : 0.005 0.044 5268 Z= 0.380 Angle : 0.650 7.096 7340 Z= 0.466 Chirality : 0.038 0.134 1030 Planarity : 0.004 0.016 1052 Dihedral : 5.922 29.573 1052 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.35 % Favored : 91.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.25), residues: 1042 helix: 0.60 (0.18), residues: 741 sheet: -1.80 (0.55), residues: 72 loop : -2.41 (0.43), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP G 5 PHE 0.000 0.000 PHE G 4 TYR 0.000 0.000 TYR G 75 *********************** 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 : 0.582 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0471 time to fit residues: 3.3974 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 : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 22 optimal weight: 50.0000 chunk 97 optimal weight: 6.9990 chunk 79 optimal weight: 30.0000 chunk 60 optimal weight: 40.0000 chunk 55 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- 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 = 0.059430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.044040 restraints weight = 62605.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.044745 restraints weight = 44825.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.045223 restraints weight = 35645.326| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5268 Z= 0.275 Angle : 0.524 4.613 7340 Z= 0.373 Chirality : 0.036 0.126 1030 Planarity : 0.003 0.018 1052 Dihedral : 5.178 24.899 1052 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.29 % Favored : 92.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1042 helix: 1.14 (0.18), residues: 735 sheet: -1.99 (0.54), residues: 72 loop : -2.31 (0.45), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP G 5 PHE 0.000 0.000 PHE G 4 TYR 0.000 0.000 TYR G 75 *********************** 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 : 0.682 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0490 time to fit residues: 3.6017 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 : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 41 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 40.0000 chunk 73 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 15 optimal weight: 50.0000 chunk 63 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 chunk 43 optimal weight: 30.0000 overall best weight: 11.5994 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.060814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.049547 restraints weight = 60421.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.048115 restraints weight = 51275.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.048556 restraints weight = 46300.797| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.6648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5268 Z= 0.333 Angle : 0.598 5.687 7340 Z= 0.427 Chirality : 0.037 0.137 1030 Planarity : 0.004 0.018 1052 Dihedral : 5.747 27.298 1052 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.27 % Favored : 89.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.26), residues: 1042 helix: 0.49 (0.18), residues: 733 sheet: -2.43 (0.56), residues: 74 loop : -2.61 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP G 5 PHE 0.000 0.000 PHE G 4 TYR 0.000 0.000 TYR G 75 *********************** 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 : 0.660 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0511 time to fit residues: 3.7050 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 : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 0.0030 chunk 10 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 89 optimal weight: 30.0000 chunk 72 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 30.0000 overall best weight: 4.7998 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.060455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.045677 restraints weight = 61374.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.046133 restraints weight = 46892.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.046645 restraints weight = 38443.087| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5268 Z= 0.155 Angle : 0.403 3.891 7340 Z= 0.278 Chirality : 0.035 0.121 1030 Planarity : 0.002 0.009 1052 Dihedral : 4.556 21.292 1052 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.47 % Favored : 94.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.27), residues: 1042 helix: 2.33 (0.17), residues: 730 sheet: -2.15 (0.58), residues: 72 loop : -1.97 (0.47), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP G 5 PHE 0.000 0.000 PHE G 4 TYR 0.000 0.000 TYR G 75 ********************** 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 : 0.664 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0595 time to fit residues: 4.2975 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 : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 40.0000 chunk 92 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 50.0000 chunk 90 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 51 optimal weight: 50.0000 chunk 101 optimal weight: 30.0000 overall best weight: 8.9592 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.061550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.049588 restraints weight = 60585.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.049275 restraints weight = 46214.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.049598 restraints weight = 38625.759| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.6633 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= 0.261 Angle : 0.501 4.376 7340 Z= 0.356 Chirality : 0.036 0.126 1030 Planarity : 0.003 0.015 1052 Dihedral : 4.972 24.338 1052 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.73 % Favored : 91.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 1042 helix: 1.75 (0.18), residues: 735 sheet: -2.28 (0.58), residues: 74 loop : -2.31 (0.46), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP G 5 PHE 0.000 0.000 PHE G 4 TYR 0.000 0.000 TYR G 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1988.65 seconds wall clock time: 35 minutes 53.34 seconds (2153.34 seconds total)