Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 14:22:35 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqi_21351/12_2021/6vqi_21351.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqi_21351/12_2021/6vqi_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_21351/12_2021/6vqi_21351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqi_21351/12_2021/6vqi_21351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqi_21351/12_2021/6vqi_21351.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqi_21351/12_2021/6vqi_21351.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/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: {'PTRANS': 8, 'TRANS': 350, 'PCIS': 1} 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: 3.70, 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 Amimo 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: 2.77 Conformation dependent library (CDL) restraints added in 1.3 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: 0.28 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: 1.92 Time building geometry restraints manager: 2.96 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 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. 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 Write .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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.380 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 20.730 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.280 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 33.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 % 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 *********************** 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 : 0.660 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0514 time to fit residues: 3.6441 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8191 ------------------------------------------------------------------------------- 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: 0.7383 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 % 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 *********************** 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 : 0.708 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0502 time to fit residues: 3.6585 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8588 ------------------------------------------------------------------------------- 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: 6.9990 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: 30.0000 chunk 91 optimal weight: 40.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- 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: 0.7489 moved from start: 0.3291 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 : 0.548 7.393 7340 Z= 0.387 Chirality : 0.036 0.153 1030 Planarity : 0.003 0.014 1052 Dihedral : 4.990 29.068 1052 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 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: 2.75 (0.24), residues: 1042 helix: 2.72 (0.16), residues: 739 sheet: 0.75 (0.63), residues: 63 loop : -0.86 (0.40), residues: 240 *********************** 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 : 0.639 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0490 time to fit residues: 3.5681 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8197 ------------------------------------------------------------------------------- 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: 8.9990 chunk 48 optimal weight: 50.0000 chunk 10 optimal weight: 0.3980 chunk 44 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 30.0000 overall best weight: 4.6788 ------------------------------------------------------------------------------- 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: 0.7443 moved from start: 0.3369 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= 0.152 Angle : 0.390 4.877 7340 Z= 0.267 Chirality : 0.035 0.144 1030 Planarity : 0.002 0.009 1052 Dihedral : 3.985 20.695 1052 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 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: 3.93 (0.25), residues: 1042 helix: 3.75 (0.16), residues: 740 sheet: 0.79 (0.58), residues: 73 loop : -1.01 (0.43), residues: 229 *********************** 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 : 0.571 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0513 time to fit residues: 3.5937 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9004 ------------------------------------------------------------------------------- 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: 0.0070 chunk 73 optimal weight: 9.9990 chunk 40 optimal weight: 40.0000 chunk 84 optimal weight: 20.0000 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: 50.0000 chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 30.0000 overall best weight: 11.2010 ------------------------------------------------------------------------------- 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: 0.7544 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 5268 Z= 0.330 Angle : 0.598 6.760 7340 Z= 0.427 Chirality : 0.036 0.144 1030 Planarity : 0.004 0.015 1052 Dihedral : 5.496 28.513 1052 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.28 % Favored : 94.63 % Rotamer Outliers : 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: 1.18 (0.25), residues: 1042 helix: 1.71 (0.17), residues: 734 sheet: -0.66 (0.54), residues: 72 loop : -1.70 (0.42), residues: 236 *********************** 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 : 0.670 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0518 time to fit residues: 3.7312 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8394 ------------------------------------------------------------------------------- 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: 40.0000 chunk 24 optimal weight: 40.0000 chunk 98 optimal weight: 30.0000 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 20.0000 chunk 51 optimal weight: 50.0000 chunk 95 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 overall best weight: 6.7590 ------------------------------------------------------------------------------- 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: 0.7498 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 5268 Z= 0.201 Angle : 0.441 4.423 7340 Z= 0.310 Chirality : 0.035 0.144 1030 Planarity : 0.003 0.011 1052 Dihedral : 4.493 22.642 1052 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 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: 2.20 (0.26), residues: 1042 helix: 2.60 (0.17), residues: 736 sheet: -1.04 (0.53), residues: 74 loop : -1.57 (0.44), residues: 232 *********************** 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 : 0.697 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0502 time to fit residues: 3.6950 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.602 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8628 ------------------------------------------------------------------------------- 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: 30.0000 chunk 83 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 39 optimal weight: 50.0000 chunk 58 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- 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: 0.7485 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 5268 Z= 0.167 Angle : 0.395 4.221 7340 Z= 0.274 Chirality : 0.035 0.144 1030 Planarity : 0.002 0.009 1052 Dihedral : 4.049 19.621 1052 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 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: 2.95 (0.26), residues: 1042 helix: 3.24 (0.17), residues: 738 sheet: -1.20 (0.54), residues: 74 loop : -1.51 (0.46), residues: 230 *********************** 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 : 0.683 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0507 time to fit residues: 3.6753 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.674 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8312 ------------------------------------------------------------------------------- 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: 30.0000 chunk 62 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 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: 40.0000 chunk 55 optimal weight: 40.0000 overall best weight: 5.5790 ------------------------------------------------------------------------------- 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: 0.7489 moved from start: 0.5307 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= 0.178 Angle : 0.401 3.390 7340 Z= 0.282 Chirality : 0.035 0.137 1030 Planarity : 0.002 0.009 1052 Dihedral : 4.043 19.369 1052 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.72 % Rotamer Outliers : 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: 2.96 (0.26), residues: 1042 helix: 3.24 (0.17), residues: 738 sheet: -1.32 (0.54), residues: 74 loop : -1.46 (0.47), residues: 230 *********************** 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 : 0.677 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0521 time to fit residues: 3.7700 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.709 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7589 ------------------------------------------------------------------------------- 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: 50.0000 chunk 71 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 40.0000 chunk 96 optimal weight: 30.0000 chunk 59 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 67 optimal weight: 30.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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: 0.7528 moved from start: 0.5664 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= 0.227 Angle : 0.453 3.917 7340 Z= 0.322 Chirality : 0.035 0.128 1030 Planarity : 0.003 0.011 1052 Dihedral : 4.465 22.509 1052 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.62 % Favored : 93.28 % Rotamer Outliers : 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: 2.22 (0.26), residues: 1042 helix: 2.70 (0.17), residues: 737 sheet: -1.49 (0.55), residues: 74 loop : -1.76 (0.46), residues: 231 *********************** 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 : 0.685 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0512 time to fit residues: 3.7299 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8217 ------------------------------------------------------------------------------- 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: 30.0000 chunk 93 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 49 optimal weight: 40.0000 chunk 64 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 50.0000 chunk 74 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- 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: 0.5910 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= 0.209 Angle : 0.438 3.492 7340 Z= 0.310 Chirality : 0.035 0.127 1030 Planarity : 0.003 0.010 1052 Dihedral : 4.401 22.065 1052 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.53 % Favored : 93.38 % Rotamer Outliers : 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: 2.13 (0.26), residues: 1042 helix: 2.69 (0.17), residues: 736 sheet: -1.74 (0.56), residues: 74 loop : -1.89 (0.46), residues: 232 ********************** 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 : 0.641 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0515 time to fit residues: 3.7391 Evaluate side-chains 29 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.610 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8079 ------------------------------------------------------------------------------- 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: 6.9990 chunk 33 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 30.0000 chunk 71 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 58 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.061110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.047209 restraints weight = 64857.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.047072 restraints weight = 53495.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.047342 restraints weight = 43406.212| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.013 5268 Z= 0.145 Angle : 0.368 3.672 7340 Z= 0.255 Chirality : 0.035 0.127 1030 Planarity : 0.002 0.008 1052 Dihedral : 3.923 18.085 1052 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.37 % Favored : 94.53 % Rotamer Outliers : 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: 3.11 (0.27), residues: 1042 helix: 3.45 (0.17), residues: 738 sheet: -1.64 (0.56), residues: 74 loop : -1.63 (0.48), residues: 230 =============================================================================== Job complete usr+sys time: 980.72 seconds wall clock time: 18 minutes 33.62 seconds (1113.62 seconds total)