Starting phenix.real_space_refine on Sat Aug 3 19:02:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bhw_44555/08_2024/9bhw_44555.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bhw_44555/08_2024/9bhw_44555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bhw_44555/08_2024/9bhw_44555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bhw_44555/08_2024/9bhw_44555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bhw_44555/08_2024/9bhw_44555.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bhw_44555/08_2024/9bhw_44555.cif" } resolution = 2.72 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= 0.007 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 40 5.16 5 C 5499 2.51 5 N 1556 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 166": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ASP 175": "OD1" <-> "OD2" Residue "D GLU 38": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8759 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1929 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 232} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2429 Classifications: {'peptide': 299} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 287} Chain: "C" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2411 Classifications: {'peptide': 297} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 285} Chain: "D" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1878 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 225} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.29, per 1000 atoms: 0.72 Number of scatterers: 8759 At special positions: 0 Unit cell: (59.778, 79.461, 180.063, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 8 15.00 O 1656 8.00 N 1556 7.00 C 5499 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: 3.29 Conformation dependent library (CDL) restraints added in 1.5 seconds 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 8 sheets defined 45.8% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 115 through 134 removed outlier: 3.831A pdb=" N SER A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 171 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 188 through 206 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.539A pdb=" N SER A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.693A pdb=" N LEU A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'B' and resid 10 through 12 No H-bonds generated for 'chain 'B' and resid 10 through 12' Processing helix chain 'B' and resid 13 through 26 removed outlier: 3.806A pdb=" N ARG B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 104 through 124 Processing helix chain 'B' and resid 151 through 162 Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 196 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 212 through 225 Processing helix chain 'B' and resid 262 through 272 removed outlier: 3.624A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 285 through 296 Processing helix chain 'C' and resid 10 through 12 No H-bonds generated for 'chain 'C' and resid 10 through 12' Processing helix chain 'C' and resid 13 through 24 removed outlier: 4.142A pdb=" N ARG C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 50 Processing helix chain 'C' and resid 104 through 124 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 178 through 196 Processing helix chain 'C' and resid 203 through 207 removed outlier: 3.513A pdb=" N LEU C 207 " --> pdb=" O LEU C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 225 removed outlier: 4.049A pdb=" N ARG C 217 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 285 through 298 Processing helix chain 'D' and resid 50 through 59 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.745A pdb=" N GLY D 92 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 133 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 188 through 206 Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 269 through 278 Processing helix chain 'D' and resid 282 through 292 Processing helix chain 'D' and resid 292 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 89 removed outlier: 6.216A pdb=" N PHE A 37 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR A 98 " --> pdb=" O PHE A 37 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE A 39 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ASP A 100 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 41 " --> pdb=" O ASP A 100 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N CYS A 148 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR A 40 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU A 150 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N MET A 42 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE A 152 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL A 44 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N CYS A 149 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU A 180 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR A 151 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 242 through 245 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 79 Processing sheet with id=AA4, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 79 removed outlier: 6.541A pdb=" N CYS C 139 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL C 170 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR C 141 " --> pdb=" O VAL C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AA7, first strand: chain 'D' and resid 82 through 88 removed outlier: 6.309A pdb=" N PHE D 37 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N THR D 98 " --> pdb=" O PHE D 37 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE D 39 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP D 100 " --> pdb=" O PHE D 39 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU D 41 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 151 " --> pdb=" O ILE D 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 242 through 245 428 hydrogen bonds defined for protein. 1173 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: 2.24 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1571 1.32 - 1.44: 2148 1.44 - 1.56: 5127 1.56 - 1.69: 12 1.69 - 1.81: 60 Bond restraints: 8918 Sorted by residual: bond pdb=" C ASP B 175 " pdb=" O ASP B 175 " ideal model delta sigma weight residual 1.236 1.199 0.036 1.29e-02 6.01e+03 7.95e+00 bond pdb=" C5 GDP B 401 " pdb=" C4 GDP B 401 " ideal model delta sigma weight residual 1.490 1.442 0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" N ASP A 185 " pdb=" CA ASP A 185 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.32e-02 5.74e+03 5.45e+00 bond pdb=" C5 GDP A 501 " pdb=" C4 GDP A 501 " ideal model delta sigma weight residual 1.490 1.448 0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" C5 GDP D 501 " pdb=" C4 GDP D 501 " ideal model delta sigma weight residual 1.490 1.450 0.040 2.00e-02 2.50e+03 4.07e+00 ... (remaining 8913 not shown) Histogram of bond angle deviations from ideal: 98.79 - 106.29: 216 106.29 - 113.79: 5225 113.79 - 121.29: 4395 121.29 - 128.79: 2162 128.79 - 136.29: 67 Bond angle restraints: 12065 Sorted by residual: angle pdb=" CA ASP B 175 " pdb=" CB ASP B 175 " pdb=" CG ASP B 175 " ideal model delta sigma weight residual 112.60 121.45 -8.85 1.00e+00 1.00e+00 7.84e+01 angle pdb=" N THR B 297 " pdb=" CA THR B 297 " pdb=" C THR B 297 " ideal model delta sigma weight residual 113.88 108.78 5.10 1.23e+00 6.61e-01 1.72e+01 angle pdb=" O1A GDP B 401 " pdb=" PA GDP B 401 " pdb=" O2A GDP B 401 " ideal model delta sigma weight residual 109.50 120.15 -10.65 3.00e+00 1.11e-01 1.26e+01 angle pdb=" N ARG A 96 " pdb=" CA ARG A 96 " pdb=" C ARG A 96 " ideal model delta sigma weight residual 107.99 101.84 6.15 1.76e+00 3.23e-01 1.22e+01 angle pdb=" C LYS A 51 " pdb=" CA LYS A 51 " pdb=" CB LYS A 51 " ideal model delta sigma weight residual 110.90 116.04 -5.14 1.58e+00 4.01e-01 1.06e+01 ... (remaining 12060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.63: 5190 26.63 - 53.26: 197 53.26 - 79.89: 27 79.89 - 106.52: 2 106.52 - 133.15: 3 Dihedral angle restraints: 5419 sinusoidal: 2303 harmonic: 3116 Sorted by residual: dihedral pdb=" C5' GDP D 501 " pdb=" O5' GDP D 501 " pdb=" PA GDP D 501 " pdb=" O3A GDP D 501 " ideal model delta sinusoidal sigma weight residual 179.98 -46.87 -133.15 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O5' GDP A 501 " pdb=" O3A GDP A 501 " pdb=" PA GDP A 501 " pdb=" PB GDP A 501 " ideal model delta sinusoidal sigma weight residual -179.98 -64.94 -115.04 1 2.00e+01 2.50e-03 3.42e+01 dihedral pdb=" C5' GDP B 401 " pdb=" O5' GDP B 401 " pdb=" PA GDP B 401 " pdb=" O3A GDP B 401 " ideal model delta sinusoidal sigma weight residual 179.98 -71.55 -108.47 1 2.00e+01 2.50e-03 3.16e+01 ... (remaining 5416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1006 0.048 - 0.095: 284 0.095 - 0.143: 76 0.143 - 0.191: 4 0.191 - 0.238: 4 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CB VAL A 79 " pdb=" CA VAL A 79 " pdb=" CG1 VAL A 79 " pdb=" CG2 VAL A 79 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA VAL A 79 " pdb=" N VAL A 79 " pdb=" C VAL A 79 " pdb=" CB VAL A 79 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ARG A 96 " pdb=" N ARG A 96 " pdb=" C ARG A 96 " pdb=" CB ARG A 96 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1371 not shown) Planarity restraints: 1529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 175 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" CG ASP B 175 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP B 175 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 175 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 246 " 0.164 9.50e-02 1.11e+02 7.37e-02 4.07e+00 pdb=" NE ARG C 246 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 246 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 246 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 246 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 267 " 0.152 9.50e-02 1.11e+02 6.87e-02 3.58e+00 pdb=" NE ARG B 267 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 267 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 267 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 267 " 0.001 2.00e-02 2.50e+03 ... (remaining 1526 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 212 2.71 - 3.25: 8470 3.25 - 3.80: 13701 3.80 - 4.35: 17826 4.35 - 4.90: 30470 Nonbonded interactions: 70679 Sorted by model distance: nonbonded pdb=" NH1 ARG A 253 " pdb=" OH TYR A 255 " model vdw 2.158 3.120 nonbonded pdb=" OE2 GLU C 116 " pdb=" OH TYR C 290 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR A 151 " pdb=" OD1 ASP A 164 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR D 151 " pdb=" OD1 ASP D 164 " model vdw 2.204 3.040 nonbonded pdb=" OE1 GLU C 69 " pdb=" NZ LYS C 71 " model vdw 2.226 3.120 ... (remaining 70674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 36 through 62 or resid 78 through 133 or resid 142 through \ 216 or resid 227 through 302 or resid 501)) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 2 through 298 or resid 401)) selection = chain 'C' } 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 individual isotropic 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: 6.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.610 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 0.050 8918 Z= 0.361 Angle : 0.715 10.645 12065 Z= 0.361 Chirality : 0.048 0.238 1374 Planarity : 0.005 0.074 1529 Dihedral : 14.136 133.149 3393 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.31 % Allowed : 0.00 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.77 (0.25), residues: 1051 helix: 1.37 (0.26), residues: 420 sheet: 0.73 (0.36), residues: 177 loop : -0.32 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 250 HIS 0.007 0.001 HIS D 147 PHE 0.019 0.002 PHE B 29 TYR 0.016 0.002 TYR B 141 ARG 0.015 0.001 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 194 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8197 (mp10) cc_final: 0.7920 (mp10) REVERT: D 124 LYS cc_start: 0.8726 (tppt) cc_final: 0.8505 (tppp) REVERT: D 128 ASP cc_start: 0.7729 (m-30) cc_final: 0.7194 (m-30) outliers start: 3 outliers final: 0 residues processed: 196 average time/residue: 1.6671 time to fit residues: 341.8854 Evaluate side-chains 80 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.0040 chunk 42 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 275 ASN B 284 GLN C 110 HIS C 114 GLN C 284 GLN D 121 HIS ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8918 Z= 0.268 Angle : 0.620 9.592 12065 Z= 0.309 Chirality : 0.045 0.160 1374 Planarity : 0.005 0.054 1529 Dihedral : 8.384 100.806 1202 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.15 % Allowed : 9.84 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.28 (0.26), residues: 1051 helix: 2.04 (0.25), residues: 424 sheet: 0.61 (0.35), residues: 185 loop : -0.17 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 115 HIS 0.006 0.001 HIS D 147 PHE 0.011 0.001 PHE D 195 TYR 0.018 0.002 TYR D 211 ARG 0.011 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: D 124 LYS cc_start: 0.8774 (tppt) cc_final: 0.8496 (tppp) REVERT: D 127 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7446 (pp20) REVERT: D 128 ASP cc_start: 0.7622 (m-30) cc_final: 0.7281 (m-30) outliers start: 21 outliers final: 5 residues processed: 107 average time/residue: 1.5970 time to fit residues: 179.7866 Evaluate side-chains 75 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 230 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8918 Z= 0.300 Angle : 0.601 8.233 12065 Z= 0.296 Chirality : 0.045 0.147 1374 Planarity : 0.004 0.054 1529 Dihedral : 8.016 85.201 1202 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.95 % Allowed : 11.37 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.52 (0.26), residues: 1051 helix: 2.33 (0.25), residues: 421 sheet: 0.59 (0.35), residues: 186 loop : -0.06 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 115 HIS 0.003 0.001 HIS D 147 PHE 0.011 0.001 PHE C 49 TYR 0.015 0.002 TYR D 151 ARG 0.013 0.001 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: D 124 LYS cc_start: 0.8819 (tppt) cc_final: 0.8425 (tppp) REVERT: D 127 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7523 (pp20) REVERT: D 128 ASP cc_start: 0.7657 (m-30) cc_final: 0.7281 (m-30) outliers start: 19 outliers final: 8 residues processed: 87 average time/residue: 1.4853 time to fit residues: 137.2169 Evaluate side-chains 86 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 230 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8918 Z= 0.252 Angle : 0.570 8.361 12065 Z= 0.280 Chirality : 0.044 0.144 1374 Planarity : 0.004 0.054 1529 Dihedral : 7.749 80.373 1202 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.95 % Allowed : 12.70 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.64 (0.26), residues: 1051 helix: 2.45 (0.25), residues: 421 sheet: 0.78 (0.36), residues: 176 loop : -0.04 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 115 HIS 0.003 0.001 HIS D 172 PHE 0.010 0.001 PHE C 49 TYR 0.013 0.002 TYR A 255 ARG 0.014 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 78 THR cc_start: 0.6190 (OUTLIER) cc_final: 0.5920 (p) REVERT: D 124 LYS cc_start: 0.8829 (tppt) cc_final: 0.8434 (tppp) REVERT: D 127 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7599 (pp20) REVERT: D 128 ASP cc_start: 0.7702 (m-30) cc_final: 0.7250 (m-30) outliers start: 19 outliers final: 8 residues processed: 93 average time/residue: 1.6510 time to fit residues: 161.8756 Evaluate side-chains 80 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 230 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN D 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8918 Z= 0.263 Angle : 0.568 7.813 12065 Z= 0.279 Chirality : 0.044 0.140 1374 Planarity : 0.004 0.055 1529 Dihedral : 7.650 78.525 1202 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.95 % Allowed : 14.14 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.74 (0.26), residues: 1051 helix: 2.51 (0.25), residues: 423 sheet: 0.90 (0.37), residues: 176 loop : -0.02 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 115 HIS 0.011 0.001 HIS A 281 PHE 0.010 0.001 PHE C 49 TYR 0.012 0.001 TYR A 129 ARG 0.014 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: D 124 LYS cc_start: 0.8862 (tppt) cc_final: 0.8445 (tppp) REVERT: D 127 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7662 (pp20) REVERT: D 128 ASP cc_start: 0.7718 (m-30) cc_final: 0.7305 (m-30) outliers start: 19 outliers final: 9 residues processed: 86 average time/residue: 1.4937 time to fit residues: 136.0537 Evaluate side-chains 84 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8918 Z= 0.267 Angle : 0.571 7.396 12065 Z= 0.281 Chirality : 0.044 0.141 1374 Planarity : 0.004 0.057 1529 Dihedral : 7.610 78.737 1202 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.54 % Allowed : 15.37 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.78 (0.26), residues: 1051 helix: 2.56 (0.25), residues: 424 sheet: 1.00 (0.37), residues: 175 loop : -0.06 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 115 HIS 0.010 0.001 HIS A 281 PHE 0.010 0.001 PHE C 49 TYR 0.011 0.001 TYR A 255 ARG 0.013 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 78 THR cc_start: 0.6067 (OUTLIER) cc_final: 0.5847 (p) REVERT: D 124 LYS cc_start: 0.8882 (tppt) cc_final: 0.8451 (tppp) REVERT: D 127 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7673 (pp20) REVERT: D 128 ASP cc_start: 0.7718 (m-30) cc_final: 0.7277 (m-30) outliers start: 15 outliers final: 8 residues processed: 91 average time/residue: 1.5591 time to fit residues: 149.9719 Evaluate side-chains 81 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN D 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8918 Z= 0.227 Angle : 0.571 7.735 12065 Z= 0.282 Chirality : 0.044 0.138 1374 Planarity : 0.004 0.057 1529 Dihedral : 7.498 77.334 1202 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.84 % Allowed : 15.68 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.79 (0.26), residues: 1051 helix: 2.57 (0.25), residues: 428 sheet: 1.02 (0.37), residues: 175 loop : -0.09 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 115 HIS 0.009 0.001 HIS A 281 PHE 0.010 0.001 PHE C 49 TYR 0.011 0.001 TYR D 151 ARG 0.012 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 78 THR cc_start: 0.6033 (OUTLIER) cc_final: 0.5827 (p) REVERT: B 16 GLU cc_start: 0.7365 (tm-30) cc_final: 0.7155 (tm-30) REVERT: D 124 LYS cc_start: 0.8879 (tppt) cc_final: 0.8433 (tppp) REVERT: D 127 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7651 (pp20) REVERT: D 128 ASP cc_start: 0.7720 (m-30) cc_final: 0.7297 (m-30) outliers start: 18 outliers final: 8 residues processed: 90 average time/residue: 1.4904 time to fit residues: 141.8527 Evaluate side-chains 81 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 30 optimal weight: 0.0170 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 96 optimal weight: 0.0020 overall best weight: 0.3226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8918 Z= 0.174 Angle : 0.559 6.621 12065 Z= 0.276 Chirality : 0.043 0.136 1374 Planarity : 0.004 0.047 1529 Dihedral : 7.251 78.283 1202 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.43 % Allowed : 16.50 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1051 helix: 2.78 (0.25), residues: 424 sheet: 1.14 (0.37), residues: 175 loop : -0.03 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 115 HIS 0.008 0.001 HIS A 281 PHE 0.008 0.001 PHE C 49 TYR 0.010 0.001 TYR A 255 ARG 0.012 0.001 ARG D 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: D 124 LYS cc_start: 0.8872 (tppt) cc_final: 0.8435 (tppp) REVERT: D 127 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7677 (pp20) REVERT: D 128 ASP cc_start: 0.7739 (m-30) cc_final: 0.7327 (m-30) outliers start: 14 outliers final: 7 residues processed: 88 average time/residue: 1.4157 time to fit residues: 132.5573 Evaluate side-chains 83 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 216 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.0470 chunk 94 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 0.0370 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN D 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8918 Z= 0.204 Angle : 0.580 7.503 12065 Z= 0.283 Chirality : 0.043 0.136 1374 Planarity : 0.004 0.051 1529 Dihedral : 7.210 76.575 1202 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.43 % Allowed : 17.32 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 2.03 (0.26), residues: 1051 helix: 2.79 (0.25), residues: 426 sheet: 1.23 (0.37), residues: 175 loop : -0.02 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 115 HIS 0.008 0.001 HIS A 281 PHE 0.009 0.001 PHE C 49 TYR 0.009 0.001 TYR C 201 ARG 0.015 0.001 ARG D 248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: D 124 LYS cc_start: 0.8880 (tppt) cc_final: 0.8430 (tppp) REVERT: D 127 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7689 (pp20) REVERT: D 128 ASP cc_start: 0.7750 (m-30) cc_final: 0.7351 (m-30) outliers start: 14 outliers final: 8 residues processed: 83 average time/residue: 1.5937 time to fit residues: 139.9465 Evaluate side-chains 79 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 230 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.0970 chunk 69 optimal weight: 0.0870 chunk 104 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8918 Z= 0.187 Angle : 0.582 7.806 12065 Z= 0.284 Chirality : 0.043 0.136 1374 Planarity : 0.004 0.064 1529 Dihedral : 7.136 75.972 1202 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.13 % Allowed : 17.32 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 2.12 (0.26), residues: 1051 helix: 2.88 (0.25), residues: 424 sheet: 1.28 (0.37), residues: 175 loop : 0.04 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 115 HIS 0.008 0.001 HIS A 281 PHE 0.009 0.001 PHE C 49 TYR 0.009 0.001 TYR A 255 ARG 0.015 0.001 ARG D 248 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: D 124 LYS cc_start: 0.8871 (tppt) cc_final: 0.8423 (tppp) REVERT: D 127 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7694 (pp20) REVERT: D 128 ASP cc_start: 0.7770 (m-30) cc_final: 0.7365 (m-30) outliers start: 11 outliers final: 7 residues processed: 80 average time/residue: 1.4434 time to fit residues: 122.5993 Evaluate side-chains 81 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 230 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 209 GLN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN D 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.067994 restraints weight = 15411.540| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.02 r_work: 0.2877 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8918 Z= 0.240 Angle : 0.582 7.735 12065 Z= 0.283 Chirality : 0.044 0.139 1374 Planarity : 0.004 0.057 1529 Dihedral : 7.221 73.347 1202 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.23 % Allowed : 17.11 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 2.06 (0.26), residues: 1051 helix: 2.79 (0.25), residues: 426 sheet: 1.27 (0.37), residues: 175 loop : 0.03 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 104 HIS 0.008 0.001 HIS A 281 PHE 0.010 0.001 PHE C 49 TYR 0.009 0.001 TYR D 151 ARG 0.014 0.001 ARG D 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3475.30 seconds wall clock time: 61 minutes 30.90 seconds (3690.90 seconds total)