Starting phenix.real_space_refine on Tue Sep 24 02:04:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/09_2024/7xmr_33302.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/09_2024/7xmr_33302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/09_2024/7xmr_33302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/09_2024/7xmr_33302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/09_2024/7xmr_33302.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/09_2024/7xmr_33302.cif" } resolution = 3.1 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= 0.004 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4250 2.51 5 N 1091 2.21 5 O 1218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6611 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2165 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 11, 'TRANS': 273} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1728 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2351 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 308} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 253 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 4, 'TRANS': 29} Chain: "L" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 114 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N LEU A 234 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 234 " occ=0.00 residue: pdb=" N ALA A 235 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 235 " occ=0.00 residue: pdb=" N GLU A 236 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 236 " occ=0.00 residue: pdb=" N ASP A 237 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASP A 237 " occ=0.00 residue: pdb=" N GLU A 238 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 238 " occ=0.00 residue: pdb=" N GLU A 239 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 239 " occ=0.00 residue: pdb=" N MET A 240 " occ=0.00 ... (3 atoms not shown) pdb=" CB MET A 240 " occ=0.00 Time building chain proxies: 5.24, per 1000 atoms: 0.79 Number of scatterers: 6611 At special positions: 0 Unit cell: (111.815, 114.95, 80.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1218 8.00 N 1091 7.00 C 4250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 14 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 861.4 milliseconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1640 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 43.2% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'R' and resid 39 through 70 removed outlier: 3.507A pdb=" N ASN R 43 " --> pdb=" O ASP R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 95 Processing helix chain 'R' and resid 95 through 105 removed outlier: 3.539A pdb=" N LEU R 105 " --> pdb=" O MET R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 146 Processing helix chain 'R' and resid 149 through 154 Processing helix chain 'R' and resid 155 through 173 Processing helix chain 'R' and resid 174 through 180 Processing helix chain 'R' and resid 203 through 217 removed outlier: 3.625A pdb=" N LEU R 215 " --> pdb=" O TYR R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 243 Processing helix chain 'R' and resid 246 through 282 removed outlier: 3.796A pdb=" N SER R 250 " --> pdb=" O LYS R 246 " (cutoff:3.500A) Proline residue: R 271 - end of helix removed outlier: 3.560A pdb=" N MET R 282 " --> pdb=" O SER R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 315 Proline residue: R 309 - end of helix removed outlier: 3.590A pdb=" N LEU R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 323 removed outlier: 3.531A pdb=" N LYS R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 33 Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.856A pdb=" N LYS A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.593A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.650A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.765A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.980A pdb=" N LEU C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 185 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.507A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.182A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.306A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.118A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.891A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190 Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.723A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.934A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 1044 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: 2.05 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2095 1.34 - 1.46: 1549 1.46 - 1.58: 3039 1.58 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 6754 Sorted by residual: bond pdb=" C ILE B 270 " pdb=" O ILE B 270 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.74e-01 bond pdb=" C LEU R 270 " pdb=" N PRO R 271 " ideal model delta sigma weight residual 1.335 1.342 -0.008 1.28e-02 6.10e+03 3.65e-01 bond pdb=" C GLY B 144 " pdb=" O GLY B 144 " ideal model delta sigma weight residual 1.230 1.237 -0.007 1.37e-02 5.33e+03 2.99e-01 bond pdb=" C ASP C 48 " pdb=" N PRO C 49 " ideal model delta sigma weight residual 1.335 1.341 -0.006 1.19e-02 7.06e+03 2.95e-01 bond pdb=" C LEU R 96 " pdb=" O LEU R 96 " ideal model delta sigma weight residual 1.238 1.244 -0.007 1.28e-02 6.10e+03 2.67e-01 ... (remaining 6749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 9023 1.15 - 2.29: 131 2.29 - 3.44: 25 3.44 - 4.58: 7 4.58 - 5.73: 7 Bond angle restraints: 9193 Sorted by residual: angle pdb=" CA LEU R 96 " pdb=" C LEU R 96 " pdb=" N PRO R 97 " ideal model delta sigma weight residual 118.44 121.60 -3.16 1.59e+00 3.96e-01 3.95e+00 angle pdb=" CA ILE B 270 " pdb=" C ILE B 270 " pdb=" N CYS B 271 " ideal model delta sigma weight residual 116.60 119.46 -2.86 1.45e+00 4.76e-01 3.90e+00 angle pdb=" N ILE R 210 " pdb=" CA ILE R 210 " pdb=" C ILE R 210 " ideal model delta sigma weight residual 113.16 110.44 2.72 1.49e+00 4.50e-01 3.33e+00 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 109.34 113.08 -3.74 2.08e+00 2.31e-01 3.23e+00 angle pdb=" N LEU R 96 " pdb=" CA LEU R 96 " pdb=" C LEU R 96 " ideal model delta sigma weight residual 109.81 113.55 -3.74 2.21e+00 2.05e-01 2.87e+00 ... (remaining 9188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 3697 17.17 - 34.35: 212 34.35 - 51.52: 35 51.52 - 68.69: 3 68.69 - 85.87: 3 Dihedral angle restraints: 3950 sinusoidal: 1418 harmonic: 2532 Sorted by residual: dihedral pdb=" CB CYS L 3 " pdb=" SG CYS L 3 " pdb=" SG CYS L 14 " pdb=" CB CYS L 14 " ideal model delta sinusoidal sigma weight residual -86.00 -130.68 44.68 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CB GLU B 215 " pdb=" CG GLU B 215 " pdb=" CD GLU B 215 " pdb=" OE1 GLU B 215 " ideal model delta sinusoidal sigma weight residual 0.00 85.87 -85.87 1 3.00e+01 1.11e-03 9.90e+00 dihedral pdb=" CB GLU C 42 " pdb=" CG GLU C 42 " pdb=" CD GLU C 42 " pdb=" OE1 GLU C 42 " ideal model delta sinusoidal sigma weight residual 0.00 -85.81 85.81 1 3.00e+01 1.11e-03 9.89e+00 ... (remaining 3947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 685 0.026 - 0.051: 257 0.051 - 0.077: 81 0.077 - 0.102: 38 0.102 - 0.128: 24 Chirality restraints: 1085 Sorted by residual: chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 1082 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO B 194 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 96 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.15e-01 pdb=" N PRO R 97 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO R 97 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 97 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 155 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.00e-01 pdb=" N PRO R 156 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO R 156 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO R 156 " 0.013 5.00e-02 4.00e+02 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1492 2.78 - 3.31: 6170 3.31 - 3.84: 10874 3.84 - 4.37: 12706 4.37 - 4.90: 22023 Nonbonded interactions: 53265 Sorted by model distance: nonbonded pdb=" OG SER B 277 " pdb=" O LEU B 318 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.287 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR R 205 " pdb=" O ALA L 1 " model vdw 2.317 3.040 nonbonded pdb=" O ARG B 52 " pdb=" NZ LYS B 89 " model vdw 2.318 3.120 ... (remaining 53260 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 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: 7.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.240 Process input model: 18.700 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 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 : 0.001 0.017 6754 Z= 0.084 Angle : 0.400 5.729 9193 Z= 0.231 Chirality : 0.036 0.128 1085 Planarity : 0.002 0.028 1148 Dihedral : 10.864 85.867 2304 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.39 (0.23), residues: 859 helix: -2.56 (0.19), residues: 349 sheet: -1.24 (0.38), residues: 155 loop : -2.21 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 63 HIS 0.006 0.001 HIS A 188 PHE 0.006 0.000 PHE R 51 TYR 0.004 0.000 TYR B 289 ARG 0.001 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 180 TYR cc_start: 0.7393 (m-80) cc_final: 0.6501 (m-10) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2196 time to fit residues: 45.4531 Evaluate side-chains 119 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 43 ASN R 146 HIS R 186 ASN ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 ASN R 304 ASN A 22 ASN A 331 ASN A 333 GLN B 62 HIS B 88 ASN B 110 ASN B 340 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6754 Z= 0.235 Angle : 0.584 7.459 9193 Z= 0.305 Chirality : 0.042 0.142 1085 Planarity : 0.004 0.046 1148 Dihedral : 3.459 24.340 921 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.43 % Allowed : 11.48 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.15 (0.27), residues: 859 helix: 0.25 (0.26), residues: 348 sheet: -1.04 (0.37), residues: 166 loop : -1.59 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.008 0.002 HIS B 311 PHE 0.011 0.001 PHE R 272 TYR 0.015 0.002 TYR R 228 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: R 180 TYR cc_start: 0.7897 (m-80) cc_final: 0.6966 (m-10) REVERT: R 241 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.7057 (ttp-170) REVERT: A 349 LYS cc_start: 0.7567 (mtpp) cc_final: 0.7342 (mttt) outliers start: 10 outliers final: 8 residues processed: 133 average time/residue: 0.1907 time to fit residues: 33.3689 Evaluate side-chains 119 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 340 ASN L 5 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6754 Z= 0.238 Angle : 0.580 7.128 9193 Z= 0.304 Chirality : 0.042 0.157 1085 Planarity : 0.004 0.043 1148 Dihedral : 3.633 21.956 921 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.15 % Allowed : 14.63 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.28), residues: 859 helix: 1.05 (0.27), residues: 349 sheet: -0.70 (0.37), residues: 167 loop : -1.36 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.005 0.001 HIS B 311 PHE 0.014 0.001 PHE R 272 TYR 0.012 0.001 TYR B 289 ARG 0.011 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: R 241 ARG cc_start: 0.7317 (ttp-170) cc_final: 0.7092 (ttp-170) REVERT: A 283 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5957 (tt) REVERT: A 349 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7336 (mttm) REVERT: B 258 ASP cc_start: 0.4363 (t0) cc_final: 0.4156 (t70) outliers start: 15 outliers final: 12 residues processed: 133 average time/residue: 0.1751 time to fit residues: 31.6359 Evaluate side-chains 127 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 PHE Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 73 optimal weight: 0.0270 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 186 ASN A 213 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6754 Z= 0.182 Angle : 0.542 7.974 9193 Z= 0.281 Chirality : 0.042 0.177 1085 Planarity : 0.003 0.041 1148 Dihedral : 3.642 20.079 921 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.01 % Allowed : 17.22 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.00 (0.28), residues: 859 helix: 1.49 (0.28), residues: 350 sheet: -0.58 (0.37), residues: 167 loop : -1.25 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.014 0.001 PHE R 272 TYR 0.013 0.001 TYR A 296 ARG 0.011 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: R 101 MET cc_start: 0.5947 (mmt) cc_final: 0.5682 (mmm) REVERT: R 241 ARG cc_start: 0.7264 (ttp-170) cc_final: 0.7055 (ttp-170) REVERT: A 349 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7364 (mttt) REVERT: B 101 MET cc_start: 0.7782 (mtp) cc_final: 0.7566 (mtp) REVERT: B 258 ASP cc_start: 0.4342 (t0) cc_final: 0.4033 (t70) outliers start: 14 outliers final: 11 residues processed: 124 average time/residue: 0.1955 time to fit residues: 32.1876 Evaluate side-chains 124 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain L residue 6 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 186 ASN A 188 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 88 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6754 Z= 0.342 Angle : 0.669 7.883 9193 Z= 0.349 Chirality : 0.045 0.157 1085 Planarity : 0.004 0.040 1148 Dihedral : 4.229 17.410 921 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.01 % Allowed : 18.08 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.29), residues: 859 helix: 1.33 (0.28), residues: 348 sheet: -0.79 (0.37), residues: 171 loop : -1.25 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.006 0.002 HIS B 54 PHE 0.016 0.002 PHE A 267 TYR 0.041 0.002 TYR B 59 ARG 0.012 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 65 ILE cc_start: 0.7338 (mm) cc_final: 0.6869 (mt) REVERT: R 101 MET cc_start: 0.5937 (mmt) cc_final: 0.5599 (mmm) REVERT: R 241 ARG cc_start: 0.7399 (ttp-170) cc_final: 0.7194 (ttp-170) REVERT: A 349 LYS cc_start: 0.7656 (mtpp) cc_final: 0.7377 (mttm) REVERT: B 101 MET cc_start: 0.8027 (mtp) cc_final: 0.7814 (mtp) REVERT: B 329 THR cc_start: 0.8807 (m) cc_final: 0.8251 (p) outliers start: 21 outliers final: 17 residues processed: 133 average time/residue: 0.1924 time to fit residues: 33.4943 Evaluate side-chains 129 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain L residue 6 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 43 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6754 Z= 0.199 Angle : 0.572 7.680 9193 Z= 0.297 Chirality : 0.042 0.161 1085 Planarity : 0.004 0.048 1148 Dihedral : 4.013 22.438 921 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.73 % Allowed : 19.37 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.29), residues: 859 helix: 1.55 (0.28), residues: 348 sheet: -0.63 (0.37), residues: 168 loop : -1.06 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.012 0.001 PHE R 272 TYR 0.015 0.002 TYR B 59 ARG 0.011 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: R 65 ILE cc_start: 0.7345 (mm) cc_final: 0.6877 (mt) REVERT: R 241 ARG cc_start: 0.7330 (ttp-170) cc_final: 0.7112 (ttp-170) REVERT: A 349 LYS cc_start: 0.7648 (mtpp) cc_final: 0.7354 (mttm) REVERT: B 101 MET cc_start: 0.7971 (mtp) cc_final: 0.7619 (mtm) REVERT: B 220 GLN cc_start: 0.7495 (mt0) cc_final: 0.7129 (mm-40) REVERT: B 329 THR cc_start: 0.8751 (m) cc_final: 0.8211 (p) outliers start: 19 outliers final: 15 residues processed: 130 average time/residue: 0.2054 time to fit residues: 34.9268 Evaluate side-chains 122 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain L residue 6 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 ASN ** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6754 Z= 0.200 Angle : 0.595 8.135 9193 Z= 0.305 Chirality : 0.043 0.232 1085 Planarity : 0.004 0.050 1148 Dihedral : 3.952 19.435 921 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.73 % Allowed : 19.80 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.13 (0.29), residues: 859 helix: 1.60 (0.28), residues: 348 sheet: -0.70 (0.36), residues: 177 loop : -1.06 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.029 0.001 PHE A 189 TYR 0.015 0.002 TYR B 59 ARG 0.011 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.762 Fit side-chains REVERT: R 65 ILE cc_start: 0.7331 (mm) cc_final: 0.6902 (mt) REVERT: R 241 ARG cc_start: 0.7328 (ttp-170) cc_final: 0.7077 (ttp-170) REVERT: A 198 MET cc_start: 0.7870 (mpp) cc_final: 0.7500 (mpp) REVERT: A 349 LYS cc_start: 0.7665 (mtpp) cc_final: 0.7383 (mttm) REVERT: B 101 MET cc_start: 0.8013 (mtp) cc_final: 0.7782 (mtp) REVERT: B 329 THR cc_start: 0.8743 (m) cc_final: 0.8201 (p) REVERT: C 46 LYS cc_start: 0.6923 (mmtt) cc_final: 0.6525 (mmtt) outliers start: 19 outliers final: 19 residues processed: 128 average time/residue: 0.2431 time to fit residues: 41.7561 Evaluate side-chains 126 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain L residue 6 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 0.0060 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6754 Z= 0.192 Angle : 0.584 8.188 9193 Z= 0.299 Chirality : 0.042 0.174 1085 Planarity : 0.004 0.051 1148 Dihedral : 3.868 17.224 921 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.16 % Allowed : 20.09 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.29), residues: 859 helix: 1.63 (0.28), residues: 348 sheet: -0.69 (0.36), residues: 178 loop : -1.03 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.019 0.001 PHE A 189 TYR 0.013 0.001 TYR B 59 ARG 0.012 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 0.640 Fit side-chains REVERT: R 65 ILE cc_start: 0.7335 (mm) cc_final: 0.6909 (mt) REVERT: R 241 ARG cc_start: 0.7314 (ttp-170) cc_final: 0.7076 (ttp-170) REVERT: A 349 LYS cc_start: 0.7813 (mtpp) cc_final: 0.7542 (mttm) REVERT: B 101 MET cc_start: 0.8049 (mtp) cc_final: 0.7808 (mtp) REVERT: B 329 THR cc_start: 0.8735 (m) cc_final: 0.8183 (p) outliers start: 22 outliers final: 19 residues processed: 127 average time/residue: 0.1849 time to fit residues: 30.9982 Evaluate side-chains 125 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain L residue 6 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 50 optimal weight: 0.0970 chunk 80 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6754 Z= 0.201 Angle : 0.598 8.302 9193 Z= 0.307 Chirality : 0.042 0.168 1085 Planarity : 0.004 0.057 1148 Dihedral : 3.894 18.197 921 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.01 % Allowed : 20.80 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.29), residues: 859 helix: 1.64 (0.28), residues: 349 sheet: -0.84 (0.35), residues: 185 loop : -0.98 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.012 0.001 PHE R 272 TYR 0.015 0.002 TYR B 59 ARG 0.012 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.704 Fit side-chains REVERT: R 65 ILE cc_start: 0.7341 (mm) cc_final: 0.6920 (mt) REVERT: R 99 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5410 (tt) REVERT: R 241 ARG cc_start: 0.7317 (ttp-170) cc_final: 0.7067 (ttp-170) REVERT: A 208 ARG cc_start: 0.7427 (ttp-110) cc_final: 0.7189 (ttp-110) REVERT: A 308 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7454 (mt-10) REVERT: A 349 LYS cc_start: 0.7816 (mtpp) cc_final: 0.7547 (mttm) REVERT: B 101 MET cc_start: 0.8121 (mtp) cc_final: 0.7811 (mtp) REVERT: B 329 THR cc_start: 0.8738 (m) cc_final: 0.8176 (p) outliers start: 21 outliers final: 20 residues processed: 123 average time/residue: 0.1858 time to fit residues: 30.4205 Evaluate side-chains 128 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain L residue 6 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.0980 chunk 38 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.0010 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6754 Z= 0.190 Angle : 0.590 8.539 9193 Z= 0.304 Chirality : 0.042 0.166 1085 Planarity : 0.004 0.054 1148 Dihedral : 3.922 18.762 921 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.16 % Allowed : 20.95 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.29), residues: 859 helix: 1.63 (0.28), residues: 350 sheet: -0.85 (0.34), residues: 185 loop : -1.03 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.011 0.001 PHE A 334 TYR 0.014 0.002 TYR B 59 ARG 0.011 0.001 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 0.692 Fit side-chains REVERT: R 65 ILE cc_start: 0.7338 (mm) cc_final: 0.6924 (mt) REVERT: R 241 ARG cc_start: 0.7301 (ttp-170) cc_final: 0.7013 (ttp-170) REVERT: A 33 GLU cc_start: 0.7531 (tt0) cc_final: 0.7285 (tt0) REVERT: A 349 LYS cc_start: 0.7811 (mtpp) cc_final: 0.7539 (mttm) REVERT: B 52 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7675 (mpt180) REVERT: B 101 MET cc_start: 0.8118 (mtp) cc_final: 0.7797 (mtp) REVERT: B 329 THR cc_start: 0.8739 (m) cc_final: 0.8200 (p) outliers start: 22 outliers final: 21 residues processed: 124 average time/residue: 0.1870 time to fit residues: 30.8907 Evaluate side-chains 127 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain L residue 6 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.0670 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.197901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.163853 restraints weight = 6996.930| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 2.13 r_work: 0.4061 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6754 Z= 0.210 Angle : 0.608 8.641 9193 Z= 0.312 Chirality : 0.043 0.169 1085 Planarity : 0.004 0.054 1148 Dihedral : 3.954 19.106 921 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.87 % Allowed : 21.09 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.29), residues: 859 helix: 1.63 (0.28), residues: 349 sheet: -0.94 (0.34), residues: 187 loop : -1.03 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.011 0.001 PHE A 334 TYR 0.015 0.002 TYR B 59 ARG 0.011 0.001 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2077.87 seconds wall clock time: 37 minutes 59.69 seconds (2279.69 seconds total)