Starting phenix.real_space_refine on Thu Mar 6 07:13:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqi_21351/03_2025/6vqi_21351.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqi_21351/03_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_21351/03_2025/6vqi_21351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqi_21351/03_2025/6vqi_21351.map" model { file = "/net/cci-nas-00/data/ceres_data/6vqi_21351/03_2025/6vqi_21351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqi_21351/03_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-5624/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: 4.15, per 1000 atoms: 0.79 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: 1.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.56 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: 1.67 Time building geometry restraints manager: 1.93 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: 2.060 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.980 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- 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 : 0.556 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0504 time to fit residues: 3.4903 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 : 0.565 ------------------------------------------------------------------------------- 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 = 0.049485 restraints weight = 61281.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.049339 restraints weight = 52601.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.049471 restraints weight = 46890.077| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 19.408 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 : 0.628 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0529 time to fit residues: 3.8036 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 : 0.562 ------------------------------------------------------------------------------- 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: 7.9990 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: 6.9990 chunk 42 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 32 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 = 0.3608 r_free = 0.3608 target = 0.063253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.048450 restraints weight = 59875.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.048923 restraints weight = 48237.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.049162 restraints weight = 41641.120| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 5268 Z= 0.164 Angle : 0.396 4.982 7340 Z= 0.272 Chirality : 0.035 0.133 1030 Planarity : 0.002 0.009 1052 Dihedral : 3.761 20.147 1052 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: 4.66 (0.25), residues: 1042 helix: 4.19 (0.15), residues: 746 sheet: 1.60 (0.60), residues: 72 loop : -0.69 (0.43), residues: 224 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 : 0.610 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0531 time to fit residues: 3.7784 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 : 0.600 ------------------------------------------------------------------------------- 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: 6.9990 chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 chunk 59 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 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 = 0.3559 r_free = 0.3559 target = 0.061811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.047432 restraints weight = 62228.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.047293 restraints weight = 50561.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.047345 restraints weight = 44520.766| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3756 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= 0.197 Angle : 0.430 5.441 7340 Z= 0.299 Chirality : 0.035 0.141 1030 Planarity : 0.002 0.010 1052 Dihedral : 4.209 21.843 1052 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.69 % Favored : 97.22 % 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: 3.84 (0.25), residues: 1042 helix: 3.52 (0.16), residues: 751 sheet: 0.95 (0.59), residues: 72 loop : -0.69 (0.46), residues: 219 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 : 0.572 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0489 time to fit residues: 3.5364 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 : 0.605 ------------------------------------------------------------------------------- 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: 40.0000 chunk 92 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 50.0000 chunk 39 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 56 optimal weight: 40.0000 chunk 65 optimal weight: 9.9990 chunk 16 optimal weight: 50.0000 chunk 72 optimal weight: 40.0000 chunk 71 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.060709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.046065 restraints weight = 61950.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.046132 restraints weight = 51688.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.046313 restraints weight = 40364.551| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4688 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= 0.251 Angle : 0.501 5.478 7340 Z= 0.352 Chirality : 0.036 0.135 1030 Planarity : 0.003 0.013 1052 Dihedral : 4.790 25.483 1052 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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: 2.41 (0.25), residues: 1042 helix: 2.64 (0.17), residues: 736 sheet: -0.13 (0.54), residues: 72 loop : -1.40 (0.44), residues: 234 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 : 0.531 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0494 time to fit residues: 3.5105 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 : 0.554 ------------------------------------------------------------------------------- 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: 9.9990 chunk 0 optimal weight: 30.0000 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 20.0000 chunk 86 optimal weight: 0.3980 chunk 82 optimal weight: 7.9990 chunk 40 optimal weight: 50.0000 chunk 22 optimal weight: 40.0000 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 overall best weight: 4.4586 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.061582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.047351 restraints weight = 62512.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.047361 restraints weight = 52892.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.047529 restraints weight = 43327.599| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 5268 Z= 0.142 Angle : 0.374 3.843 7340 Z= 0.257 Chirality : 0.035 0.139 1030 Planarity : 0.002 0.009 1052 Dihedral : 3.922 19.149 1052 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: 3.57 (0.26), residues: 1042 helix: 3.59 (0.16), residues: 739 sheet: -0.21 (0.53), residues: 74 loop : -1.21 (0.45), 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 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 : 0.603 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0499 time to fit residues: 3.5497 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 : 0.569 ------------------------------------------------------------------------------- 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: 10.0000 chunk 37 optimal weight: 20.0000 chunk 21 optimal weight: 50.0000 chunk 1 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 overall best weight: 11.5996 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.059894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.046008 restraints weight = 60262.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.046178 restraints weight = 49972.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.046229 restraints weight = 39354.324| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5561 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= 0.340 Angle : 0.580 5.878 7340 Z= 0.418 Chirality : 0.037 0.132 1030 Planarity : 0.004 0.014 1052 Dihedral : 5.249 27.584 1052 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % 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: 1.04 (0.25), residues: 1042 helix: 1.70 (0.17), residues: 737 sheet: -1.17 (0.52), residues: 74 loop : -2.01 (0.43), residues: 231 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 : 0.573 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0496 time to fit residues: 3.4853 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 50.0000 chunk 5 optimal weight: 3.9990 chunk 57 optimal weight: 30.0000 chunk 94 optimal weight: 30.0000 chunk 74 optimal weight: 0.1980 chunk 22 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 79 optimal weight: 30.0000 chunk 60 optimal weight: 30.0000 chunk 55 optimal weight: 30.0000 chunk 91 optimal weight: 30.0000 overall best weight: 10.2390 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.061708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.049245 restraints weight = 59479.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.048945 restraints weight = 43736.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.049147 restraints weight = 42984.696| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.5989 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= 0.292 Angle : 0.528 4.500 7340 Z= 0.379 Chirality : 0.036 0.124 1030 Planarity : 0.003 0.014 1052 Dihedral : 5.028 24.473 1052 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.43 % Favored : 93.47 % 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: 0.81 (0.26), residues: 1042 helix: 1.64 (0.18), residues: 732 sheet: -1.86 (0.52), residues: 76 loop : -2.20 (0.44), residues: 234 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 : 0.851 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0624 time to fit residues: 4.4067 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 : 0.630 ------------------------------------------------------------------------------- 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: 30.0000 chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 40.0000 chunk 73 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 15 optimal weight: 50.0000 chunk 63 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 43 optimal weight: 30.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.059810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.045003 restraints weight = 62924.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.045591 restraints weight = 47076.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.045906 restraints weight = 38867.848| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.6318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5268 Z= 0.250 Angle : 0.495 4.273 7340 Z= 0.351 Chirality : 0.036 0.125 1030 Planarity : 0.003 0.013 1052 Dihedral : 4.960 24.583 1052 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.58 % Favored : 92.23 % 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: 0.98 (0.26), residues: 1042 helix: 1.79 (0.18), residues: 733 sheet: -1.94 (0.54), residues: 74 loop : -2.19 (0.46), 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 : 0.615 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0517 time to fit residues: 3.6921 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 : 0.611 ------------------------------------------------------------------------------- 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: 8.9990 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 40.0000 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 30.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.062418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.050108 restraints weight = 60540.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.049558 restraints weight = 51541.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.049643 restraints weight = 42006.144| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5268 Z= 0.161 Angle : 0.397 3.556 7340 Z= 0.276 Chirality : 0.035 0.121 1030 Planarity : 0.002 0.009 1052 Dihedral : 4.376 19.989 1052 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.74 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: 2.19 (0.27), residues: 1042 helix: 2.75 (0.17), residues: 731 sheet: -1.84 (0.54), residues: 74 loop : -1.80 (0.47), 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 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 : 0.570 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0476 time to fit residues: 3.3981 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 : 0.550 ------------------------------------------------------------------------------- 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: 7.9990 chunk 32 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 51 optimal weight: 40.0000 chunk 101 optimal weight: 30.0000 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 = 0.3520 r_free = 0.3520 target = 0.060162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.045305 restraints weight = 64123.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.045870 restraints weight = 48399.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.046261 restraints weight = 40034.441| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5268 Z= 0.218 Angle : 0.447 3.717 7340 Z= 0.317 Chirality : 0.035 0.122 1030 Planarity : 0.003 0.011 1052 Dihedral : 4.568 22.155 1052 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.87 % Favored : 92.03 % 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: 1.72 (0.27), residues: 1042 helix: 2.46 (0.17), residues: 731 sheet: -1.92 (0.56), residues: 74 loop : -2.22 (0.45), 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2005.66 seconds wall clock time: 35 minutes 7.60 seconds (2107.60 seconds total)