Starting phenix.real_space_refine on Mon Apr 28 03:43:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0q_39711/04_2025/8z0q_39711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0q_39711/04_2025/8z0q_39711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z0q_39711/04_2025/8z0q_39711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0q_39711/04_2025/8z0q_39711.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0q_39711/04_2025/8z0q_39711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0q_39711/04_2025/8z0q_39711.cif" } resolution = 2.6 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= 0.036 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 16 5.16 5 C 4367 2.51 5 N 1231 2.21 5 O 1267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6881 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3398 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 29, 'TRANS': 408} Unresolved chain links: 1 Unresolved chain link angles: 5 Unresolved chain link dihedrals: 7 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 3483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3483 Classifications: {'peptide': 446} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 415} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 4.87, per 1000 atoms: 0.71 Number of scatterers: 6881 At special positions: 0 Unit cell: (68.04, 91.56, 105, 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 16 16.00 O 1267 8.00 N 1231 7.00 C 4367 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: 1.60 Conformation dependent library (CDL) restraints added in 961.8 milliseconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1652 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 42.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.692A pdb=" N SER C 117 " --> pdb=" O CYS C 114 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU C 118 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU C 119 " --> pdb=" O GLN C 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 114 through 119' Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 194 through 206 Processing helix chain 'C' and resid 242 through 262 removed outlier: 4.424A pdb=" N ARG C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 286 Processing helix chain 'C' and resid 288 through 302 Processing helix chain 'C' and resid 334 through 347 removed outlier: 3.674A pdb=" N ARG C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 364 Processing helix chain 'C' and resid 365 through 367 No H-bonds generated for 'chain 'C' and resid 365 through 367' Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.630A pdb=" N LEU C 386 " --> pdb=" O ARG C 383 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 408 through 426 removed outlier: 3.501A pdb=" N HIS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 439 Processing helix chain 'C' and resid 512 through 533 removed outlier: 3.509A pdb=" N VAL C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 547 removed outlier: 4.242A pdb=" N ASP C 547 " --> pdb=" O GLU C 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 removed outlier: 4.191A pdb=" N GLU D 118 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D 119 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 242 through 262 removed outlier: 4.419A pdb=" N ARG D 262 " --> pdb=" O GLN D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 289 through 302 Processing helix chain 'D' and resid 333 through 348 Processing helix chain 'D' and resid 350 through 364 Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 384 through 389 removed outlier: 3.501A pdb=" N GLU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG D 388 " --> pdb=" O GLU D 385 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 389 " --> pdb=" O LEU D 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 389' Processing helix chain 'D' and resid 408 through 425 removed outlier: 3.515A pdb=" N LEU D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 439 Processing helix chain 'D' and resid 512 through 533 removed outlier: 3.582A pdb=" N LEU D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 546 Processing sheet with id=AA1, first strand: chain 'C' and resid 188 through 191 removed outlier: 6.488A pdb=" N ALA C 188 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR C 224 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU C 190 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA C 138 " --> pdb=" O LEU C 478 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 166 through 171 Processing sheet with id=AA3, first strand: chain 'C' and resid 325 through 333 removed outlier: 3.665A pdb=" N GLU C 495 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N VAL C 452 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA C 373 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N PHE C 454 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY C 375 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LEU C 456 " --> pdb=" O GLY C 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'D' and resid 188 through 191 removed outlier: 6.896A pdb=" N ALA D 188 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR D 224 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU D 190 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N THR D 226 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 225 " --> pdb=" O GLU D 229 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 325 through 332 removed outlier: 6.057A pdb=" N MET D 453 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL D 493 " --> pdb=" O MET D 453 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASN D 455 " --> pdb=" O VAL D 493 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLU D 495 " --> pdb=" O ASN D 455 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL D 457 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL D 452 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU D 456 " --> pdb=" O PRO D 377 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR D 379 " --> pdb=" O LEU D 456 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.83 Time building geometry restraints manager: 1.94 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: 2333 1.34 - 1.46: 1484 1.46 - 1.58: 3201 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 7046 Sorted by residual: bond pdb=" C TYR C 446 " pdb=" N SER C 447 " ideal model delta sigma weight residual 1.331 1.364 -0.033 3.12e-02 1.03e+03 1.11e+00 bond pdb=" CA THR D 226 " pdb=" C THR D 226 " ideal model delta sigma weight residual 1.517 1.525 -0.009 1.02e-02 9.61e+03 7.21e-01 bond pdb=" CA PHE C 450 " pdb=" CB PHE C 450 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.68e-01 bond pdb=" C THR C 226 " pdb=" N PRO C 227 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.19e-02 7.06e+03 5.00e-01 bond pdb=" C ASP C 498 " pdb=" N GLY C 499 " ideal model delta sigma weight residual 1.319 1.331 -0.011 1.64e-02 3.72e+03 4.78e-01 ... (remaining 7041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 9501 1.96 - 3.93: 96 3.93 - 5.89: 8 5.89 - 7.85: 0 7.85 - 9.82: 1 Bond angle restraints: 9606 Sorted by residual: angle pdb=" C TYR C 446 " pdb=" N SER C 447 " pdb=" CA SER C 447 " ideal model delta sigma weight residual 120.69 130.51 -9.82 2.95e+00 1.15e-01 1.11e+01 angle pdb=" N GLY C 499 " pdb=" CA GLY C 499 " pdb=" C GLY C 499 " ideal model delta sigma weight residual 110.29 114.39 -4.10 1.28e+00 6.10e-01 1.03e+01 angle pdb=" C GLU D 118 " pdb=" N LEU D 119 " pdb=" CA LEU D 119 " ideal model delta sigma weight residual 121.54 116.42 5.12 1.91e+00 2.74e-01 7.18e+00 angle pdb=" C PRO C 448 " pdb=" N LEU C 449 " pdb=" CA LEU C 449 " ideal model delta sigma weight residual 121.54 126.01 -4.47 1.91e+00 2.74e-01 5.48e+00 angle pdb=" C PRO D 448 " pdb=" N LEU D 449 " pdb=" CA LEU D 449 " ideal model delta sigma weight residual 121.54 125.75 -4.21 1.91e+00 2.74e-01 4.85e+00 ... (remaining 9601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 3835 16.78 - 33.57: 312 33.57 - 50.35: 65 50.35 - 67.13: 12 67.13 - 83.91: 5 Dihedral angle restraints: 4229 sinusoidal: 1664 harmonic: 2565 Sorted by residual: dihedral pdb=" CA ASP D 509 " pdb=" CB ASP D 509 " pdb=" CG ASP D 509 " pdb=" OD1 ASP D 509 " ideal model delta sinusoidal sigma weight residual -30.00 -90.16 60.16 1 2.00e+01 2.50e-03 1.21e+01 dihedral pdb=" CG ARG C 342 " pdb=" CD ARG C 342 " pdb=" NE ARG C 342 " pdb=" CZ ARG C 342 " ideal model delta sinusoidal sigma weight residual 180.00 -135.01 -44.99 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG D 165 " pdb=" CD ARG D 165 " pdb=" NE ARG D 165 " pdb=" CZ ARG D 165 " ideal model delta sinusoidal sigma weight residual -180.00 -136.09 -43.91 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 4226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 637 0.026 - 0.052: 268 0.052 - 0.079: 82 0.079 - 0.105: 61 0.105 - 0.131: 23 Chirality restraints: 1071 Sorted by residual: chirality pdb=" CA VAL C 234 " pdb=" N VAL C 234 " pdb=" C VAL C 234 " pdb=" CB VAL C 234 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA PHE C 286 " pdb=" N PHE C 286 " pdb=" C PHE C 286 " pdb=" CB PHE C 286 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA VAL D 429 " pdb=" N VAL D 429 " pdb=" C VAL D 429 " pdb=" CB VAL D 429 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 1068 not shown) Planarity restraints: 1268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 211 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO C 212 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 268 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO D 269 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 269 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 269 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 496 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO D 497 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 497 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 497 " 0.024 5.00e-02 4.00e+02 ... (remaining 1265 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 402 2.74 - 3.28: 6523 3.28 - 3.82: 11649 3.82 - 4.36: 13702 4.36 - 4.90: 23776 Nonbonded interactions: 56052 Sorted by model distance: nonbonded pdb=" O ALA D 159 " pdb=" NH1 ARG D 165 " model vdw 2.194 3.120 nonbonded pdb=" OH TYR C 275 " pdb=" O TYR C 392 " model vdw 2.196 3.040 nonbonded pdb=" O TYR D 132 " pdb=" NH2 ARG D 206 " model vdw 2.243 3.120 nonbonded pdb=" NH1 ARG C 381 " pdb=" O LEU C 386 " model vdw 2.277 3.120 nonbonded pdb=" O GLN C 324 " pdb=" OG1 THR C 508 " model vdw 2.297 3.040 ... (remaining 56047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 101 through 117 or (resid 118 and (name N or name CA or na \ me C or name O )) or resid 119 through 264 or (resid 265 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 266 through 292 or (resid \ 293 and (name N or name CA or name C or name O or name CB )) or resid 294 throug \ h 303 or (resid 304 and (name N or name CA or name C or name O or name CB )) or \ resid 305 through 367 or (resid 368 and (name N or name CA or name C or name O o \ r name CB or name CG )) or resid 369 or (resid 370 through 371 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD )) or resid 372 throu \ gh 432 or (resid 433 and (name N or name CA or name C or name O or name CB )) or \ resid 434 through 459 or (resid 460 and (name N or name CA or name C or name CB \ )) or (resid 471 and (name C or name O )) or resid 472 through 539 or (resid 54 \ 0 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name NE )) or resid 541 through 542 or (resid 543 and (name N or name CA or nam \ e C or name O or name CB or name CG )) or (resid 544 through 547 and (name N or \ name CA or name C or name O or name CB )) or (resid 548 and (name N )))) } 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: 2.270 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: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.110 Find NCS groups from input model: 0.230 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:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 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 : 0.002 0.033 7046 Z= 0.101 Angle : 0.493 9.816 9606 Z= 0.261 Chirality : 0.039 0.131 1071 Planarity : 0.005 0.054 1268 Dihedral : 13.183 83.913 2577 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.97 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.58 (0.28), residues: 874 helix: 1.78 (0.29), residues: 338 sheet: -0.05 (0.34), residues: 212 loop : -0.75 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 120 HIS 0.002 0.001 HIS D 424 PHE 0.019 0.002 PHE D 241 TYR 0.012 0.001 TYR D 257 ARG 0.003 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.17405 ( 344) hydrogen bonds : angle 6.07351 ( 999) covalent geometry : bond 0.00213 ( 7046) covalent geometry : angle 0.49301 ( 9606) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.731 Fit side-chains REVERT: C 217 MET cc_start: 0.7501 (mmt) cc_final: 0.7263 (mmm) REVERT: C 383 ARG cc_start: 0.5130 (mmt-90) cc_final: 0.3265 (mtm180) REVERT: D 205 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6201 (tm-30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 1.5105 time to fit residues: 146.9719 Evaluate side-chains 69 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 0.0040 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN D 366 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.209150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.176238 restraints weight = 6333.591| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 1.99 r_work: 0.3959 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7046 Z= 0.126 Angle : 0.544 6.602 9606 Z= 0.282 Chirality : 0.041 0.141 1071 Planarity : 0.005 0.048 1268 Dihedral : 4.038 15.524 990 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.20 % Favored : 96.68 % Rotamer: Outliers : 1.97 % Allowed : 6.20 % Favored : 91.83 % 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: 0.72 (0.28), residues: 874 helix: 1.82 (0.28), residues: 343 sheet: 0.10 (0.34), residues: 214 loop : -0.69 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 120 HIS 0.003 0.001 HIS D 424 PHE 0.021 0.002 PHE D 241 TYR 0.011 0.001 TYR D 257 ARG 0.003 0.000 ARG C 342 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 344) hydrogen bonds : angle 4.72745 ( 999) covalent geometry : bond 0.00275 ( 7046) covalent geometry : angle 0.54383 ( 9606) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.842 Fit side-chains REVERT: C 140 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7792 (ttm110) REVERT: C 283 ARG cc_start: 0.3876 (ttp-170) cc_final: 0.3210 (mmt-90) REVERT: D 139 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7183 (p90) REVERT: D 205 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6286 (tm-30) outliers start: 14 outliers final: 5 residues processed: 84 average time/residue: 1.3935 time to fit residues: 123.2340 Evaluate side-chains 73 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 14 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.0030 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 HIS C 415 GLN C 417 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.208092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.173922 restraints weight = 6462.449| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.01 r_work: 0.3935 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7046 Z= 0.125 Angle : 0.533 7.501 9606 Z= 0.276 Chirality : 0.041 0.159 1071 Planarity : 0.005 0.046 1268 Dihedral : 4.038 15.431 990 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.55 % Favored : 96.34 % Rotamer: Outliers : 1.69 % Allowed : 10.00 % Favored : 88.31 % 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: 0.81 (0.28), residues: 874 helix: 1.95 (0.28), residues: 338 sheet: 0.17 (0.35), residues: 206 loop : -0.67 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 120 HIS 0.003 0.001 HIS D 424 PHE 0.021 0.002 PHE D 241 TYR 0.011 0.001 TYR D 257 ARG 0.003 0.000 ARG C 152 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 344) hydrogen bonds : angle 4.55724 ( 999) covalent geometry : bond 0.00275 ( 7046) covalent geometry : angle 0.53296 ( 9606) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.759 Fit side-chains REVERT: D 205 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6358 (tm-30) REVERT: D 501 ARG cc_start: 0.8124 (mmp-170) cc_final: 0.7833 (mmp-170) outliers start: 12 outliers final: 6 residues processed: 82 average time/residue: 1.4282 time to fit residues: 124.4243 Evaluate side-chains 71 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN C 417 GLN D 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.203792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.169787 restraints weight = 6510.561| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.92 r_work: 0.3889 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7046 Z= 0.186 Angle : 0.614 7.935 9606 Z= 0.321 Chirality : 0.043 0.150 1071 Planarity : 0.006 0.047 1268 Dihedral : 4.423 17.520 990 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 2.25 % Allowed : 12.96 % Favored : 84.79 % 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: 0.49 (0.28), residues: 874 helix: 1.61 (0.28), residues: 344 sheet: 0.05 (0.36), residues: 195 loop : -0.80 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 120 HIS 0.004 0.001 HIS C 230 PHE 0.025 0.003 PHE D 241 TYR 0.015 0.002 TYR D 323 ARG 0.003 0.000 ARG D 219 Details of bonding type rmsd hydrogen bonds : bond 0.04854 ( 344) hydrogen bonds : angle 4.77320 ( 999) covalent geometry : bond 0.00416 ( 7046) covalent geometry : angle 0.61424 ( 9606) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.718 Fit side-chains REVERT: C 383 ARG cc_start: 0.5362 (mmt-90) cc_final: 0.3171 (mtm180) REVERT: D 205 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6545 (tm-30) REVERT: D 501 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7182 (mmp-170) outliers start: 16 outliers final: 6 residues processed: 77 average time/residue: 1.2063 time to fit residues: 98.2887 Evaluate side-chains 72 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN C 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.205169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.172737 restraints weight = 6411.165| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 1.69 r_work: 0.3904 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7046 Z= 0.140 Angle : 0.547 6.919 9606 Z= 0.285 Chirality : 0.041 0.133 1071 Planarity : 0.005 0.049 1268 Dihedral : 4.223 17.550 990 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.22 % Rotamer: Outliers : 1.97 % Allowed : 14.37 % Favored : 83.66 % 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 (0.28), residues: 874 helix: 1.73 (0.28), residues: 344 sheet: 0.17 (0.36), residues: 202 loop : -0.78 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 120 HIS 0.003 0.001 HIS C 230 PHE 0.023 0.002 PHE D 241 TYR 0.013 0.002 TYR D 257 ARG 0.003 0.000 ARG D 219 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 344) hydrogen bonds : angle 4.53333 ( 999) covalent geometry : bond 0.00312 ( 7046) covalent geometry : angle 0.54688 ( 9606) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.826 Fit side-chains REVERT: D 205 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6387 (tm-30) REVERT: D 501 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7211 (mmp-170) outliers start: 14 outliers final: 6 residues processed: 74 average time/residue: 1.1763 time to fit residues: 92.3537 Evaluate side-chains 68 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 7 optimal weight: 0.0570 chunk 67 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.0670 chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 36 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.209473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.177672 restraints weight = 6490.476| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.75 r_work: 0.3973 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7046 Z= 0.095 Angle : 0.483 5.991 9606 Z= 0.249 Chirality : 0.040 0.122 1071 Planarity : 0.005 0.049 1268 Dihedral : 3.874 15.705 990 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.97 % Favored : 96.91 % Rotamer: Outliers : 1.55 % Allowed : 15.49 % Favored : 82.96 % 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: 0.93 (0.28), residues: 874 helix: 1.97 (0.28), residues: 344 sheet: 0.33 (0.36), residues: 199 loop : -0.61 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 120 HIS 0.002 0.001 HIS D 216 PHE 0.019 0.002 PHE D 241 TYR 0.010 0.001 TYR D 257 ARG 0.003 0.000 ARG D 381 Details of bonding type rmsd hydrogen bonds : bond 0.03227 ( 344) hydrogen bonds : angle 4.22660 ( 999) covalent geometry : bond 0.00210 ( 7046) covalent geometry : angle 0.48345 ( 9606) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.752 Fit side-chains REVERT: D 205 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6357 (tm-30) REVERT: D 501 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7842 (mmp-170) outliers start: 11 outliers final: 8 residues processed: 80 average time/residue: 1.8307 time to fit residues: 153.7266 Evaluate side-chains 75 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 85 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN C 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.207625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.175058 restraints weight = 6390.703| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.75 r_work: 0.3935 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7046 Z= 0.120 Angle : 0.516 6.415 9606 Z= 0.267 Chirality : 0.041 0.120 1071 Planarity : 0.005 0.049 1268 Dihedral : 3.979 16.959 990 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.45 % Rotamer: Outliers : 2.25 % Allowed : 15.49 % Favored : 82.25 % 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: 0.92 (0.28), residues: 874 helix: 1.96 (0.28), residues: 344 sheet: 0.34 (0.36), residues: 199 loop : -0.63 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 120 HIS 0.002 0.001 HIS C 230 PHE 0.021 0.002 PHE D 241 TYR 0.011 0.001 TYR D 257 ARG 0.002 0.000 ARG D 299 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 344) hydrogen bonds : angle 4.32407 ( 999) covalent geometry : bond 0.00268 ( 7046) covalent geometry : angle 0.51561 ( 9606) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.671 Fit side-chains REVERT: C 178 LYS cc_start: 0.6199 (OUTLIER) cc_final: 0.5840 (ttpt) REVERT: D 205 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6505 (tm-30) REVERT: D 501 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7885 (mmp-170) outliers start: 16 outliers final: 7 residues processed: 74 average time/residue: 1.2679 time to fit residues: 100.4548 Evaluate side-chains 72 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 83 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.208349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.176280 restraints weight = 6437.952| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 1.74 r_work: 0.3948 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7046 Z= 0.106 Angle : 0.492 6.393 9606 Z= 0.255 Chirality : 0.040 0.121 1071 Planarity : 0.005 0.049 1268 Dihedral : 3.901 15.916 990 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.86 % Favored : 97.03 % Rotamer: Outliers : 1.97 % Allowed : 15.92 % Favored : 82.11 % 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: 0.97 (0.28), residues: 874 helix: 1.98 (0.28), residues: 344 sheet: 0.37 (0.37), residues: 199 loop : -0.57 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 120 HIS 0.002 0.001 HIS C 230 PHE 0.019 0.002 PHE D 241 TYR 0.011 0.001 TYR D 257 ARG 0.002 0.000 ARG D 381 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 344) hydrogen bonds : angle 4.24828 ( 999) covalent geometry : bond 0.00235 ( 7046) covalent geometry : angle 0.49230 ( 9606) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.710 Fit side-chains REVERT: C 178 LYS cc_start: 0.6151 (OUTLIER) cc_final: 0.5794 (ttpt) REVERT: D 205 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6540 (tm-30) REVERT: D 501 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7902 (mmp-170) outliers start: 14 outliers final: 9 residues processed: 77 average time/residue: 1.1655 time to fit residues: 95.1892 Evaluate side-chains 78 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN C 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.205957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.173224 restraints weight = 6524.731| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.90 r_work: 0.3931 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7046 Z= 0.135 Angle : 0.537 7.206 9606 Z= 0.278 Chirality : 0.041 0.121 1071 Planarity : 0.005 0.049 1268 Dihedral : 4.077 16.451 990 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.22 % Rotamer: Outliers : 1.97 % Allowed : 16.48 % Favored : 81.55 % 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: 0.86 (0.28), residues: 874 helix: 1.88 (0.28), residues: 344 sheet: 0.28 (0.36), residues: 202 loop : -0.61 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 120 HIS 0.003 0.001 HIS C 230 PHE 0.021 0.002 PHE D 241 TYR 0.012 0.002 TYR D 323 ARG 0.003 0.000 ARG D 219 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 344) hydrogen bonds : angle 4.39100 ( 999) covalent geometry : bond 0.00303 ( 7046) covalent geometry : angle 0.53663 ( 9606) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.785 Fit side-chains REVERT: C 178 LYS cc_start: 0.6246 (OUTLIER) cc_final: 0.5856 (ttpt) REVERT: D 205 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6441 (tm-30) REVERT: D 501 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7899 (mmp-170) outliers start: 14 outliers final: 8 residues processed: 72 average time/residue: 1.4976 time to fit residues: 115.7335 Evaluate side-chains 73 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 11 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 0.0000 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 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 = 0.4410 r_free = 0.4410 target = 0.207549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.173846 restraints weight = 6554.463| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 1.83 r_work: 0.3944 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7046 Z= 0.112 Angle : 0.506 6.994 9606 Z= 0.261 Chirality : 0.041 0.123 1071 Planarity : 0.005 0.050 1268 Dihedral : 3.956 16.152 990 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.45 % Rotamer: Outliers : 1.69 % Allowed : 16.62 % Favored : 81.69 % 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: 0.91 (0.28), residues: 874 helix: 1.93 (0.28), residues: 344 sheet: 0.34 (0.37), residues: 199 loop : -0.62 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 120 HIS 0.003 0.001 HIS D 216 PHE 0.019 0.002 PHE D 241 TYR 0.011 0.001 TYR D 257 ARG 0.003 0.000 ARG D 381 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 344) hydrogen bonds : angle 4.28336 ( 999) covalent geometry : bond 0.00250 ( 7046) covalent geometry : angle 0.50630 ( 9606) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.738 Fit side-chains REVERT: C 178 LYS cc_start: 0.6161 (OUTLIER) cc_final: 0.5794 (ttpt) REVERT: D 205 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6384 (tm-30) REVERT: D 501 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7902 (mmp-170) outliers start: 12 outliers final: 9 residues processed: 71 average time/residue: 1.6520 time to fit residues: 124.3106 Evaluate side-chains 75 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 80 optimal weight: 0.0970 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN C 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.207341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.174949 restraints weight = 6493.642| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 1.92 r_work: 0.3948 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7046 Z= 0.116 Angle : 0.513 7.377 9606 Z= 0.264 Chirality : 0.041 0.120 1071 Planarity : 0.005 0.049 1268 Dihedral : 3.958 16.143 990 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.32 % Favored : 96.57 % Rotamer: Outliers : 1.83 % Allowed : 16.48 % Favored : 81.69 % 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: 0.90 (0.28), residues: 874 helix: 1.93 (0.28), residues: 344 sheet: 0.30 (0.37), residues: 199 loop : -0.61 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 120 HIS 0.003 0.001 HIS D 216 PHE 0.019 0.002 PHE D 241 TYR 0.011 0.001 TYR D 257 ARG 0.003 0.000 ARG D 381 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 344) hydrogen bonds : angle 4.28054 ( 999) covalent geometry : bond 0.00258 ( 7046) covalent geometry : angle 0.51303 ( 9606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5921.20 seconds wall clock time: 106 minutes 55.78 seconds (6415.78 seconds total)