Starting phenix.real_space_refine on Thu Nov 14 23:08:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isy_35700/11_2024/8isy_35700.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isy_35700/11_2024/8isy_35700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isy_35700/11_2024/8isy_35700.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isy_35700/11_2024/8isy_35700.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isy_35700/11_2024/8isy_35700.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isy_35700/11_2024/8isy_35700.cif" } resolution = 3.27 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= 0.009 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 23 5.16 5 C 5096 2.51 5 N 1308 2.21 5 O 1450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7877 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4117 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 478} Chain: "B" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3760 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 435} Time building chain proxies: 5.03, per 1000 atoms: 0.64 Number of scatterers: 7877 At special positions: 0 Unit cell: (82.82, 104.14, 117.26, 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 23 16.00 O 1450 8.00 N 1308 7.00 C 5096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1826 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 42.9% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.738A pdb=" N TYR A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.668A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TYR A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 205 through 216 removed outlier: 4.557A pdb=" N GLU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 248 through 264 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 366 through 376 removed outlier: 3.855A pdb=" N VAL A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 477 through 482 removed outlier: 4.301A pdb=" N PHE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.846A pdb=" N TYR A 505 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 28 removed outlier: 3.740A pdb=" N THR B 18 " --> pdb=" O ASP B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 44 through 56 removed outlier: 4.670A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 109 through 114 removed outlier: 4.111A pdb=" N ARG B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 138 Processing helix chain 'B' and resid 146 through 159 removed outlier: 3.971A pdb=" N SER B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 227 through 233 removed outlier: 3.945A pdb=" N THR B 232 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 257 through 280 Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'B' and resid 353 through 367 removed outlier: 3.522A pdb=" N GLN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN B 367 " --> pdb=" O LYS B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 384 Processing helix chain 'B' and resid 421 through 436 removed outlier: 4.238A pdb=" N ASP B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE B 433 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 4.056A pdb=" N LEU B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.787A pdb=" N CYS A 299 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL A 317 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA A 297 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY A 385 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE A 412 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLU A 3 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS B 413 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N TYR A 6 " --> pdb=" O LYS B 413 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N SER B 415 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET B 414 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS B 167 " --> pdb=" O MET B 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 95 removed outlier: 6.254A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 removed outlier: 3.654A pdb=" N GLU A 327 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.603A pdb=" N SER A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.047A pdb=" N ILE B 5 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS B 4 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LEU B 61 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE B 6 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL B 63 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER B 8 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE B 95 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE B 60 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU B 97 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 62 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ILE B 118 " --> pdb=" O ILE B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 283 through 286 removed outlier: 6.706A pdb=" N PHE B 291 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA B 325 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 283 through 286 removed outlier: 6.706A pdb=" N PHE B 291 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA B 325 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 402 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 208 through 210 Processing sheet with id=AB1, first strand: chain 'B' and resid 304 through 305 353 hydrogen bonds defined for protein. 975 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: 2.69 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2285 1.33 - 1.45: 1241 1.45 - 1.57: 4510 1.57 - 1.69: 0 1.69 - 1.80: 35 Bond restraints: 8071 Sorted by residual: bond pdb=" N TYR B 318 " pdb=" CA TYR B 318 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.21e-02 6.83e+03 8.40e+00 bond pdb=" CA SER A 175 " pdb=" CB SER A 175 " ideal model delta sigma weight residual 1.528 1.489 0.039 1.37e-02 5.33e+03 8.26e+00 bond pdb=" N LYS B 317 " pdb=" CA LYS B 317 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.15e-02 7.56e+03 8.18e+00 bond pdb=" N GLU A 184 " pdb=" CA GLU A 184 " ideal model delta sigma weight residual 1.457 1.492 -0.036 1.28e-02 6.10e+03 7.79e+00 bond pdb=" N GLU B 13 " pdb=" CA GLU B 13 " ideal model delta sigma weight residual 1.452 1.486 -0.034 1.22e-02 6.72e+03 7.72e+00 ... (remaining 8066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 10617 1.68 - 3.35: 244 3.35 - 5.03: 32 5.03 - 6.71: 8 6.71 - 8.38: 4 Bond angle restraints: 10905 Sorted by residual: angle pdb=" CA PHE A 183 " pdb=" C PHE A 183 " pdb=" O PHE A 183 " ideal model delta sigma weight residual 122.03 115.16 6.87 1.17e+00 7.31e-01 3.45e+01 angle pdb=" N VAL B 395 " pdb=" CA VAL B 395 " pdb=" C VAL B 395 " ideal model delta sigma weight residual 113.71 108.34 5.37 9.50e-01 1.11e+00 3.20e+01 angle pdb=" C ASP B 191 " pdb=" CA ASP B 191 " pdb=" CB ASP B 191 " ideal model delta sigma weight residual 116.54 110.80 5.74 1.15e+00 7.56e-01 2.49e+01 angle pdb=" C PHE A 183 " pdb=" CA PHE A 183 " pdb=" CB PHE A 183 " ideal model delta sigma weight residual 111.95 104.90 7.05 1.50e+00 4.44e-01 2.21e+01 angle pdb=" N LYS A 174 " pdb=" CA LYS A 174 " pdb=" C LYS A 174 " ideal model delta sigma weight residual 112.38 107.11 5.27 1.22e+00 6.72e-01 1.86e+01 ... (remaining 10900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4481 17.56 - 35.13: 313 35.13 - 52.69: 50 52.69 - 70.26: 18 70.26 - 87.82: 6 Dihedral angle restraints: 4868 sinusoidal: 2045 harmonic: 2823 Sorted by residual: dihedral pdb=" CB MET A 406 " pdb=" CG MET A 406 " pdb=" SD MET A 406 " pdb=" CE MET A 406 " ideal model delta sinusoidal sigma weight residual -60.00 -0.13 -59.87 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB LYS B 196 " pdb=" CG LYS B 196 " pdb=" CD LYS B 196 " pdb=" CE LYS B 196 " ideal model delta sinusoidal sigma weight residual 60.00 119.05 -59.05 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG ARG A 275 " pdb=" CD ARG A 275 " pdb=" NE ARG A 275 " pdb=" CZ ARG A 275 " ideal model delta sinusoidal sigma weight residual 90.00 131.68 -41.68 2 1.50e+01 4.44e-03 9.43e+00 ... (remaining 4865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 898 0.048 - 0.096: 194 0.096 - 0.144: 72 0.144 - 0.192: 5 0.192 - 0.240: 2 Chirality restraints: 1171 Sorted by residual: chirality pdb=" CA LEU A 182 " pdb=" N LEU A 182 " pdb=" C LEU A 182 " pdb=" CB LEU A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA GLU A 185 " pdb=" N GLU A 185 " pdb=" C GLU A 185 " pdb=" CB GLU A 185 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA GLU B 13 " pdb=" N GLU B 13 " pdb=" C GLU B 13 " pdb=" CB GLU B 13 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1168 not shown) Planarity restraints: 1387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 178 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C TYR A 178 " -0.043 2.00e-02 2.50e+03 pdb=" O TYR A 178 " 0.016 2.00e-02 2.50e+03 pdb=" N THR A 179 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 19 " -0.170 9.50e-02 1.11e+02 7.64e-02 3.58e+00 pdb=" NE ARG B 19 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 19 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 19 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 19 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 177 " 0.148 9.50e-02 1.11e+02 6.64e-02 2.74e+00 pdb=" NE ARG A 177 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 177 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 177 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 177 " 0.006 2.00e-02 2.50e+03 ... (remaining 1384 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 80 2.62 - 3.19: 6447 3.19 - 3.76: 11304 3.76 - 4.33: 16885 4.33 - 4.90: 27845 Nonbonded interactions: 62561 Sorted by model distance: nonbonded pdb=" O TRP A 269 " pdb=" OH TYR A 467 " model vdw 2.047 3.040 nonbonded pdb=" O PHE A 183 " pdb=" CG GLU A 184 " model vdw 2.175 3.440 nonbonded pdb=" O ASN A 34 " pdb=" OH TYR A 261 " model vdw 2.180 3.040 nonbonded pdb=" OD2 ASP A 25 " pdb=" OH TYR B 154 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR B 66 " pdb=" OD2 ASP B 100 " model vdw 2.261 3.040 ... (remaining 62556 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=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: 0.600 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.600 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 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 : 0.004 0.039 8071 Z= 0.282 Angle : 0.604 8.382 10905 Z= 0.378 Chirality : 0.047 0.240 1171 Planarity : 0.005 0.076 1387 Dihedral : 12.788 87.820 3042 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % 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: 0.64 (0.27), residues: 953 helix: 1.39 (0.28), residues: 338 sheet: 0.75 (0.41), residues: 170 loop : -0.42 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 20 HIS 0.005 0.001 HIS B 9 PHE 0.014 0.001 PHE A 425 TYR 0.023 0.001 TYR B 416 ARG 0.003 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.987 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1767 time to fit residues: 29.6906 Evaluate side-chains 78 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS A 430 GLN A 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8071 Z= 0.293 Angle : 0.541 7.815 10905 Z= 0.289 Chirality : 0.044 0.226 1171 Planarity : 0.004 0.057 1387 Dihedral : 4.129 18.162 1036 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.83 % Favored : 97.06 % Rotamer: Outliers : 1.97 % Allowed : 8.71 % Favored : 89.31 % 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: 1.11 (0.27), residues: 953 helix: 2.22 (0.29), residues: 331 sheet: 0.71 (0.42), residues: 149 loop : -0.31 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 294 HIS 0.005 0.001 HIS B 320 PHE 0.019 0.002 PHE A 186 TYR 0.016 0.002 TYR B 330 ARG 0.005 0.001 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 1.043 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 99 average time/residue: 0.1886 time to fit residues: 26.7524 Evaluate side-chains 79 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.0570 chunk 26 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 69 optimal weight: 0.1980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8071 Z= 0.137 Angle : 0.475 7.115 10905 Z= 0.250 Chirality : 0.043 0.190 1171 Planarity : 0.004 0.052 1387 Dihedral : 3.941 17.715 1036 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.05 % Allowed : 9.64 % Favored : 89.31 % 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: 1.24 (0.27), residues: 953 helix: 2.17 (0.28), residues: 350 sheet: 0.74 (0.40), residues: 156 loop : -0.19 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 294 HIS 0.004 0.001 HIS B 9 PHE 0.027 0.001 PHE B 120 TYR 0.010 0.001 TYR B 330 ARG 0.003 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 1.030 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 97 average time/residue: 0.1712 time to fit residues: 25.2789 Evaluate side-chains 81 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8071 Z= 0.327 Angle : 0.542 6.626 10905 Z= 0.285 Chirality : 0.044 0.205 1171 Planarity : 0.004 0.047 1387 Dihedral : 4.109 19.162 1036 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.36 % Favored : 96.54 % Rotamer: Outliers : 1.63 % Allowed : 10.34 % Favored : 88.04 % 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: 1.23 (0.27), residues: 953 helix: 2.27 (0.28), residues: 344 sheet: 0.60 (0.41), residues: 144 loop : -0.20 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 294 HIS 0.005 0.001 HIS A 207 PHE 0.021 0.002 PHE A 186 TYR 0.012 0.001 TYR A 262 ARG 0.007 0.001 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 1.018 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.1824 time to fit residues: 22.2792 Evaluate side-chains 74 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8071 Z= 0.240 Angle : 0.497 7.805 10905 Z= 0.260 Chirality : 0.044 0.212 1171 Planarity : 0.004 0.046 1387 Dihedral : 4.099 20.710 1036 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 1.51 % Allowed : 10.57 % Favored : 87.92 % 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: 1.34 (0.27), residues: 953 helix: 2.29 (0.28), residues: 346 sheet: 0.57 (0.41), residues: 151 loop : -0.05 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 294 HIS 0.003 0.001 HIS A 207 PHE 0.018 0.001 PHE A 186 TYR 0.016 0.001 TYR A 472 ARG 0.003 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 1.024 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 80 average time/residue: 0.1541 time to fit residues: 18.8820 Evaluate side-chains 75 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 18 optimal weight: 0.0370 chunk 53 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8071 Z= 0.137 Angle : 0.471 10.591 10905 Z= 0.242 Chirality : 0.043 0.238 1171 Planarity : 0.003 0.041 1387 Dihedral : 3.938 19.043 1036 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.05 % Allowed : 11.50 % Favored : 87.46 % 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: 1.45 (0.28), residues: 953 helix: 2.38 (0.28), residues: 352 sheet: 0.64 (0.42), residues: 151 loop : -0.03 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 294 HIS 0.002 0.001 HIS A 207 PHE 0.013 0.001 PHE A 186 TYR 0.013 0.001 TYR A 472 ARG 0.002 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.939 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 85 average time/residue: 0.1734 time to fit residues: 22.0336 Evaluate side-chains 76 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8071 Z= 0.251 Angle : 0.518 10.447 10905 Z= 0.266 Chirality : 0.045 0.288 1171 Planarity : 0.004 0.045 1387 Dihedral : 4.049 20.150 1036 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Rotamer: Outliers : 1.28 % Allowed : 11.73 % Favored : 86.99 % 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: 1.35 (0.28), residues: 953 helix: 2.32 (0.28), residues: 351 sheet: 0.57 (0.41), residues: 151 loop : -0.08 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 294 HIS 0.004 0.001 HIS A 207 PHE 0.018 0.001 PHE A 186 TYR 0.019 0.001 TYR A 346 ARG 0.002 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.071 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 80 average time/residue: 0.1735 time to fit residues: 21.0143 Evaluate side-chains 78 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8071 Z= 0.163 Angle : 0.492 12.061 10905 Z= 0.249 Chirality : 0.044 0.343 1171 Planarity : 0.003 0.044 1387 Dihedral : 3.966 20.475 1036 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.83 % Favored : 97.06 % Rotamer: Outliers : 0.93 % Allowed : 11.73 % Favored : 87.34 % 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: 1.39 (0.28), residues: 953 helix: 2.34 (0.28), residues: 353 sheet: 0.58 (0.42), residues: 151 loop : -0.07 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 294 HIS 0.003 0.001 HIS A 207 PHE 0.019 0.001 PHE A 186 TYR 0.013 0.001 TYR A 472 ARG 0.002 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 1.013 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 78 average time/residue: 0.1788 time to fit residues: 20.9408 Evaluate side-chains 77 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.0970 chunk 87 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8071 Z= 0.177 Angle : 0.497 12.117 10905 Z= 0.251 Chirality : 0.044 0.360 1171 Planarity : 0.004 0.045 1387 Dihedral : 3.942 19.799 1036 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.17 % Rotamer: Outliers : 1.05 % Allowed : 12.31 % Favored : 86.64 % 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: 1.40 (0.28), residues: 953 helix: 2.37 (0.28), residues: 353 sheet: 0.59 (0.42), residues: 149 loop : -0.07 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 294 HIS 0.003 0.001 HIS A 207 PHE 0.032 0.001 PHE A 425 TYR 0.018 0.001 TYR B 416 ARG 0.002 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.034 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 81 average time/residue: 0.1738 time to fit residues: 21.5487 Evaluate side-chains 81 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.0670 chunk 62 optimal weight: 10.0000 chunk 94 optimal weight: 0.0870 chunk 87 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 0.0970 chunk 46 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 0.0060 chunk 23 optimal weight: 2.9990 overall best weight: 0.2310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8071 Z= 0.121 Angle : 0.488 12.996 10905 Z= 0.244 Chirality : 0.044 0.366 1171 Planarity : 0.003 0.037 1387 Dihedral : 3.775 19.825 1036 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.93 % Allowed : 12.20 % Favored : 86.88 % 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: 1.52 (0.28), residues: 953 helix: 2.52 (0.28), residues: 352 sheet: 0.71 (0.43), residues: 149 loop : -0.07 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP B 294 HIS 0.002 0.001 HIS A 207 PHE 0.021 0.001 PHE A 186 TYR 0.028 0.001 TYR A 472 ARG 0.003 0.000 ARG A 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 1.030 Fit side-chains REVERT: A 430 GLN cc_start: 0.7690 (mp10) cc_final: 0.7332 (mm110) outliers start: 8 outliers final: 7 residues processed: 88 average time/residue: 0.1789 time to fit residues: 22.8334 Evaluate side-chains 80 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** 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 = 0.3035 r_free = 0.3035 target = 0.102960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.096133 restraints weight = 32452.383| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 4.04 r_work: 0.2833 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8071 Z= 0.165 Angle : 0.493 12.832 10905 Z= 0.248 Chirality : 0.044 0.357 1171 Planarity : 0.003 0.037 1387 Dihedral : 3.800 20.178 1036 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.81 % Allowed : 12.43 % Favored : 86.76 % 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: 1.55 (0.28), residues: 953 helix: 2.51 (0.28), residues: 353 sheet: 0.71 (0.43), residues: 149 loop : -0.02 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP B 294 HIS 0.003 0.001 HIS A 207 PHE 0.027 0.001 PHE A 503 TYR 0.018 0.001 TYR A 178 ARG 0.002 0.000 ARG A 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1759.52 seconds wall clock time: 33 minutes 0.36 seconds (1980.36 seconds total)