Starting phenix.real_space_refine on Fri Apr 5 20:12:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqi_21351/04_2024/6vqi_21351.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqi_21351/04_2024/6vqi_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqi_21351/04_2024/6vqi_21351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqi_21351/04_2024/6vqi_21351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqi_21351/04_2024/6vqi_21351.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqi_21351/04_2024/6vqi_21351.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 3.68, per 1000 atoms: 0.70 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 - 3.50 Amino acid : False - 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: 2.76 Conformation dependent library (CDL) restraints added in 1.5 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: 0.54 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: 1.78 Time building geometry restraints manager: 2.54 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: 97.66 - 103.91: 27 103.91 - 110.16: 1112 110.16 - 116.41: 2370 116.41 - 122.66: 3332 122.66 - 128.91: 499 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 2.520 nonbonded pdb=" O HIS G 23 " pdb=" N THR G 27 " model vdw 2.371 2.520 nonbonded pdb=" O GLN G 275 " pdb=" N LEU G 279 " model vdw 2.386 2.520 nonbonded pdb=" N PHE a 170 " pdb=" O ILE a 221 " model vdw 2.411 2.520 nonbonded pdb=" O SER G 160 " pdb=" N ARG G 164 " model vdw 2.425 2.520 ... (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 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: 1.630 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: 8.150 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.450 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.210 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.612 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0499 time to fit residues: 3.5085 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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: 6.9990 chunk 79 optimal weight: 0.0040 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 50.0000 chunk 59 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 overall best weight: 5.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5268 Z= 0.195 Angle : 0.443 5.806 7340 Z= 0.303 Chirality : 0.036 0.125 1030 Planarity : 0.003 0.014 1052 Dihedral : 4.117 20.066 1052 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.08 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: 4.28 (0.24), residues: 1042 helix: 3.79 (0.15), residues: 748 sheet: 1.52 (0.59), residues: 69 loop : -0.38 (0.42), residues: 225 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 fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.608 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0475 time to fit residues: 3.3999 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 40.0000 chunk 28 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 91 optimal weight: 40.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 5268 Z= 0.295 Angle : 0.566 7.210 7340 Z= 0.399 Chirality : 0.036 0.160 1030 Planarity : 0.004 0.016 1052 Dihedral : 5.157 30.125 1052 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.98 % Favored : 96.83 % 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: 2.36 (0.24), residues: 1042 helix: 2.42 (0.17), residues: 738 sheet: 0.69 (0.61), residues: 65 loop : -0.99 (0.39), residues: 239 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 fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.751 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0546 time to fit residues: 4.2001 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 5.9990 chunk 48 optimal weight: 50.0000 chunk 10 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 chunk 88 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 5268 Z= 0.182 Angle : 0.425 5.124 7340 Z= 0.295 Chirality : 0.035 0.148 1030 Planarity : 0.002 0.010 1052 Dihedral : 4.247 21.825 1052 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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: 3.34 (0.25), residues: 1042 helix: 3.26 (0.16), residues: 740 sheet: 0.33 (0.56), residues: 74 loop : -0.91 (0.44), residues: 228 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 fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.706 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0604 time to fit residues: 4.2344 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.0980 chunk 73 optimal weight: 20.0000 chunk 40 optimal weight: 40.0000 chunk 84 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 50.0000 chunk 88 optimal weight: 40.0000 chunk 24 optimal weight: 40.0000 chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 overall best weight: 11.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5268 Z= 0.340 Angle : 0.603 6.651 7340 Z= 0.430 Chirality : 0.036 0.144 1030 Planarity : 0.004 0.015 1052 Dihedral : 5.627 27.755 1052 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.85 % Favored : 94.05 % 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: 0.88 (0.25), residues: 1042 helix: 1.47 (0.17), residues: 740 sheet: -0.81 (0.55), residues: 72 loop : -1.87 (0.42), residues: 230 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 fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.614 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0473 time to fit residues: 3.4986 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. 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 57 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 40.0000 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 50.0000 chunk 95 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5268 Z= 0.196 Angle : 0.441 4.482 7340 Z= 0.309 Chirality : 0.035 0.144 1030 Planarity : 0.003 0.011 1052 Dihedral : 4.597 22.642 1052 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % 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: 2.05 (0.26), residues: 1042 helix: 2.49 (0.17), residues: 736 sheet: -1.12 (0.53), residues: 74 loop : -1.67 (0.43), 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 fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.644 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0519 time to fit residues: 3.7301 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 40.0000 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 chunk 39 optimal weight: 40.0000 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5139 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= 0.165 Angle : 0.395 4.150 7340 Z= 0.274 Chirality : 0.035 0.139 1030 Planarity : 0.002 0.009 1052 Dihedral : 4.063 19.308 1052 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % 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: 2.84 (0.26), residues: 1042 helix: 3.18 (0.17), residues: 738 sheet: -1.36 (0.54), residues: 74 loop : -1.57 (0.45), residues: 230 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 fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.588 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0502 time to fit residues: 3.6238 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.3980 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 40.0000 chunk 48 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 94 optimal weight: 30.0000 chunk 85 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5268 Z= 0.184 Angle : 0.411 3.473 7340 Z= 0.289 Chirality : 0.035 0.129 1030 Planarity : 0.002 0.010 1052 Dihedral : 4.233 20.430 1052 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.37 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.67 (0.26), residues: 1042 helix: 3.03 (0.17), residues: 738 sheet: -1.44 (0.53), residues: 74 loop : -1.58 (0.47), residues: 230 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 fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.643 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0475 time to fit residues: 3.5404 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 91 optimal weight: 0.0370 chunk 60 optimal weight: 40.0000 chunk 96 optimal weight: 0.9990 chunk 59 optimal weight: 30.0000 chunk 45 optimal weight: 10.0000 chunk 67 optimal weight: 40.0000 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5593 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= 0.150 Angle : 0.371 3.678 7340 Z= 0.258 Chirality : 0.035 0.127 1030 Planarity : 0.002 0.008 1052 Dihedral : 3.918 18.104 1052 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.57 % Favored : 94.34 % 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: 3.18 (0.27), residues: 1042 helix: 3.46 (0.17), residues: 738 sheet: -1.35 (0.54), residues: 74 loop : -1.56 (0.47), residues: 230 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 fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.644 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0506 time to fit residues: 3.6420 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 80 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 49 optimal weight: 40.0000 chunk 64 optimal weight: 8.9990 chunk 86 optimal weight: 30.0000 chunk 24 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5268 Z= 0.321 Angle : 0.572 5.842 7340 Z= 0.413 Chirality : 0.036 0.124 1030 Planarity : 0.004 0.016 1052 Dihedral : 5.252 26.070 1052 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.35 % Favored : 91.55 % 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: 0.60 (0.26), residues: 1042 helix: 1.51 (0.18), residues: 736 sheet: -1.94 (0.55), residues: 74 loop : -2.43 (0.43), 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 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 fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.630 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0468 time to fit residues: 3.4676 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 50.0000 chunk 81 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 10 optimal weight: 0.3980 chunk 14 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 overall best weight: 5.8788 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.062512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.050219 restraints weight = 58948.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.049732 restraints weight = 45490.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.050023 restraints weight = 41498.012| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5268 Z= 0.178 Angle : 0.412 3.485 7340 Z= 0.288 Chirality : 0.035 0.125 1030 Planarity : 0.002 0.009 1052 Dihedral : 4.428 21.256 1052 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.53 % Favored : 93.38 % 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: 1.98 (0.26), residues: 1042 helix: 2.60 (0.17), residues: 736 sheet: -1.91 (0.55), residues: 74 loop : -2.00 (0.46), 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1094.85 seconds wall clock time: 20 minutes 25.55 seconds (1225.55 seconds total)