Starting phenix.real_space_refine on Wed Sep 17 08:00:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0q_39711/09_2025/8z0q_39711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0q_39711/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8z0q_39711/09_2025/8z0q_39711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0q_39711/09_2025/8z0q_39711.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z0q_39711/09_2025/8z0q_39711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0q_39711/09_2025/8z0q_39711.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ASP:plan': 6, 'ARG:plan': 3} 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: 1.79, per 1000 atoms: 0.26 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: 0.57 Conformation dependent library (CDL) restraints added in 461.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.25 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: 1.12 Time building geometry restraints manager: 0.79 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.210 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.120 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG C 219 TYR 0.012 0.001 TYR D 257 PHE 0.019 0.002 PHE D 241 TRP 0.011 0.001 TRP C 120 HIS 0.002 0.001 HIS D 424 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 7046) covalent geometry : angle 0.49301 ( 9606) hydrogen bonds : bond 0.17405 ( 344) hydrogen bonds : angle 6.07351 ( 999) *********************** 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 : 0.255 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: 0.7092 time to fit residues: 68.9608 Evaluate side-chains 68 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 366 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.204244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.170283 restraints weight = 6408.176| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 1.98 r_work: 0.3903 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7046 Z= 0.192 Angle : 0.634 8.174 9606 Z= 0.332 Chirality : 0.044 0.153 1071 Planarity : 0.006 0.052 1268 Dihedral : 4.418 18.093 990 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.45 % Rotamer: Outliers : 2.11 % Allowed : 6.62 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.28), residues: 874 helix: 1.49 (0.28), residues: 345 sheet: -0.00 (0.35), residues: 203 loop : -0.93 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 219 TYR 0.015 0.002 TYR D 323 PHE 0.026 0.003 PHE D 241 TRP 0.012 0.002 TRP D 281 HIS 0.005 0.001 HIS D 424 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 7046) covalent geometry : angle 0.63370 ( 9606) hydrogen bonds : bond 0.05117 ( 344) hydrogen bonds : angle 4.96426 ( 999) *********************** 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 82 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.257 Fit side-chains REVERT: C 140 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7898 (ttm110) REVERT: C 283 ARG cc_start: 0.4132 (ttp-170) cc_final: 0.3335 (mmt-90) REVERT: C 383 ARG cc_start: 0.5333 (mmt-90) cc_final: 0.3179 (mtm180) REVERT: D 205 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6677 (tm-30) REVERT: D 418 ARG cc_start: 0.6388 (mtm110) cc_final: 0.6167 (ttm-80) outliers start: 15 outliers final: 6 residues processed: 79 average time/residue: 0.6469 time to fit residues: 53.5785 Evaluate side-chains 70 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 56 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 2 optimal weight: 0.0670 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.207686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.174215 restraints weight = 6414.825| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.12 r_work: 0.3944 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1503 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= 0.119 Angle : 0.521 6.270 9606 Z= 0.272 Chirality : 0.041 0.129 1071 Planarity : 0.005 0.048 1268 Dihedral : 4.104 16.118 990 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.32 % Favored : 96.57 % Rotamer: Outliers : 2.25 % Allowed : 9.86 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.28), residues: 874 helix: 1.61 (0.28), residues: 350 sheet: 0.15 (0.36), residues: 201 loop : -0.76 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 152 TYR 0.012 0.001 TYR D 257 PHE 0.021 0.002 PHE D 241 TRP 0.010 0.001 TRP C 120 HIS 0.002 0.001 HIS D 424 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7046) covalent geometry : angle 0.52092 ( 9606) hydrogen bonds : bond 0.03944 ( 344) hydrogen bonds : angle 4.58724 ( 999) *********************** 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 88 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.317 Fit side-chains REVERT: D 205 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6477 (tm-30) REVERT: D 418 ARG cc_start: 0.6332 (mtm110) cc_final: 0.6132 (ttm-80) REVERT: D 501 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7813 (mmp-170) outliers start: 16 outliers final: 7 residues processed: 81 average time/residue: 0.5966 time to fit residues: 50.8995 Evaluate side-chains 75 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 2 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 D 490 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.208191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.175678 restraints weight = 6447.723| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 1.76 r_work: 0.3951 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3825 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.1668 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= 0.114 Angle : 0.510 6.324 9606 Z= 0.265 Chirality : 0.041 0.129 1071 Planarity : 0.005 0.046 1268 Dihedral : 4.021 15.226 990 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.45 % Rotamer: Outliers : 1.83 % Allowed : 12.96 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.28), residues: 874 helix: 1.73 (0.28), residues: 350 sheet: 0.23 (0.36), residues: 204 loop : -0.67 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 152 TYR 0.011 0.001 TYR D 257 PHE 0.020 0.002 PHE D 241 TRP 0.011 0.001 TRP C 120 HIS 0.002 0.001 HIS D 424 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7046) covalent geometry : angle 0.51040 ( 9606) hydrogen bonds : bond 0.03746 ( 344) hydrogen bonds : angle 4.46236 ( 999) *********************** 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 81 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.307 Fit side-chains REVERT: D 205 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6548 (tm-30) REVERT: D 501 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7874 (mmp-170) outliers start: 13 outliers final: 7 residues processed: 76 average time/residue: 0.6202 time to fit residues: 49.6135 Evaluate side-chains 71 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 193 THR 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 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 C 455 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.207089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.174394 restraints weight = 6523.799| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 1.77 r_work: 0.3934 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1768 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= 0.129 Angle : 0.527 7.001 9606 Z= 0.274 Chirality : 0.041 0.131 1071 Planarity : 0.005 0.046 1268 Dihedral : 4.074 16.162 990 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.22 % Rotamer: Outliers : 2.25 % Allowed : 14.23 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.28), residues: 874 helix: 1.84 (0.28), residues: 344 sheet: 0.23 (0.36), residues: 202 loop : -0.71 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 152 TYR 0.012 0.002 TYR D 257 PHE 0.021 0.002 PHE D 241 TRP 0.010 0.002 TRP C 120 HIS 0.003 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7046) covalent geometry : angle 0.52726 ( 9606) hydrogen bonds : bond 0.03902 ( 344) hydrogen bonds : angle 4.47304 ( 999) *********************** 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 82 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.294 Fit side-chains REVERT: D 205 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6366 (tm-30) REVERT: D 501 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7903 (mmp-170) outliers start: 16 outliers final: 9 residues processed: 76 average time/residue: 0.5586 time to fit residues: 45.0895 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 : 0.277 ------------------------------------------------------------------------------- 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 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 193 THR 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 24 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.205232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.172690 restraints weight = 6502.682| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 1.75 r_work: 0.3912 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1903 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= 0.152 Angle : 0.557 7.170 9606 Z= 0.290 Chirality : 0.042 0.133 1071 Planarity : 0.005 0.047 1268 Dihedral : 4.208 17.014 990 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 2.68 % Allowed : 14.51 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.28), residues: 874 helix: 1.78 (0.28), residues: 344 sheet: 0.13 (0.35), residues: 202 loop : -0.75 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 152 TYR 0.013 0.002 TYR D 323 PHE 0.022 0.002 PHE D 241 TRP 0.010 0.002 TRP C 120 HIS 0.004 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7046) covalent geometry : angle 0.55669 ( 9606) hydrogen bonds : bond 0.04205 ( 344) hydrogen bonds : angle 4.55452 ( 999) *********************** 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 86 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.277 Fit side-chains REVERT: D 205 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6376 (tm-30) REVERT: D 501 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7159 (mmp-170) outliers start: 19 outliers final: 9 residues processed: 79 average time/residue: 0.5482 time to fit residues: 45.9988 Evaluate side-chains 74 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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 193 THR 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 3 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4395 r_free = 0.4395 target = 0.205900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.173833 restraints weight = 6456.210| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 1.68 r_work: 0.3926 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 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 : 0.003 0.040 7046 Z= 0.134 Angle : 0.537 6.801 9606 Z= 0.280 Chirality : 0.041 0.131 1071 Planarity : 0.005 0.049 1268 Dihedral : 4.147 17.612 990 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.32 % Favored : 96.57 % Rotamer: Outliers : 2.39 % Allowed : 15.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.28), residues: 874 helix: 1.82 (0.28), residues: 344 sheet: 0.11 (0.35), residues: 202 loop : -0.74 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 152 TYR 0.012 0.002 TYR D 257 PHE 0.022 0.002 PHE D 241 TRP 0.009 0.001 TRP C 120 HIS 0.003 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7046) covalent geometry : angle 0.53746 ( 9606) hydrogen bonds : bond 0.03910 ( 344) hydrogen bonds : angle 4.46841 ( 999) *********************** 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 83 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.262 Fit side-chains REVERT: C 178 LYS cc_start: 0.6237 (OUTLIER) cc_final: 0.5839 (ttpt) REVERT: D 205 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6366 (tm-30) REVERT: D 501 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7140 (mmp-170) outliers start: 17 outliers final: 8 residues processed: 76 average time/residue: 0.5798 time to fit residues: 46.7564 Evaluate side-chains 75 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 193 THR 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 48 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.0000 chunk 70 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 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** 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 = 0.4407 r_free = 0.4407 target = 0.207284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.175242 restraints weight = 6514.975| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.75 r_work: 0.3937 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1992 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= 0.114 Angle : 0.515 6.920 9606 Z= 0.267 Chirality : 0.041 0.127 1071 Planarity : 0.005 0.049 1268 Dihedral : 4.026 17.389 990 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 1.97 % Allowed : 15.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.28), residues: 874 helix: 1.92 (0.28), residues: 344 sheet: 0.17 (0.35), residues: 202 loop : -0.68 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 299 TYR 0.011 0.001 TYR D 257 PHE 0.020 0.002 PHE D 241 TRP 0.011 0.001 TRP C 120 HIS 0.002 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 7046) covalent geometry : angle 0.51514 ( 9606) hydrogen bonds : bond 0.03608 ( 344) hydrogen bonds : angle 4.36078 ( 999) *********************** 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 81 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.269 Fit side-chains REVERT: C 178 LYS cc_start: 0.6151 (OUTLIER) cc_final: 0.5773 (ttpt) REVERT: D 205 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6346 (tm-30) outliers start: 14 outliers final: 9 residues processed: 76 average time/residue: 0.4856 time to fit residues: 39.3872 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 : 0.198 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 80 optimal weight: 0.0270 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.206430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.174847 restraints weight = 6498.418| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 1.71 r_work: 0.3938 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2029 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= 0.117 Angle : 0.516 6.991 9606 Z= 0.266 Chirality : 0.041 0.128 1071 Planarity : 0.005 0.049 1268 Dihedral : 4.007 16.009 990 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.45 % Rotamer: Outliers : 1.83 % Allowed : 16.34 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.28), residues: 874 helix: 1.91 (0.28), residues: 344 sheet: 0.20 (0.36), residues: 199 loop : -0.69 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 152 TYR 0.012 0.001 TYR D 257 PHE 0.021 0.002 PHE D 241 TRP 0.010 0.001 TRP C 120 HIS 0.002 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7046) covalent geometry : angle 0.51585 ( 9606) hydrogen bonds : bond 0.03655 ( 344) hydrogen bonds : angle 4.38138 ( 999) *********************** 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 73 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.258 Fit side-chains REVERT: C 178 LYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5800 (ttpt) REVERT: D 205 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6357 (tm-30) outliers start: 13 outliers final: 10 residues processed: 68 average time/residue: 0.4463 time to fit residues: 32.4095 Evaluate side-chains 72 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 330 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 32 optimal weight: 0.0870 chunk 50 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4411 r_free = 0.4411 target = 0.207774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.176040 restraints weight = 6509.282| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 1.72 r_work: 0.3949 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2092 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= 0.109 Angle : 0.505 7.061 9606 Z= 0.260 Chirality : 0.041 0.128 1071 Planarity : 0.005 0.049 1268 Dihedral : 3.936 15.939 990 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.20 % Favored : 96.68 % Rotamer: Outliers : 1.83 % Allowed : 16.76 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.28), residues: 874 helix: 1.95 (0.28), residues: 344 sheet: 0.23 (0.36), residues: 199 loop : -0.66 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 152 TYR 0.012 0.001 TYR D 257 PHE 0.020 0.002 PHE D 241 TRP 0.011 0.001 TRP C 120 HIS 0.002 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7046) covalent geometry : angle 0.50548 ( 9606) hydrogen bonds : bond 0.03490 ( 344) hydrogen bonds : angle 4.32614 ( 999) ********************** 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 79 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.287 Fit side-chains REVERT: C 178 LYS cc_start: 0.6158 (OUTLIER) cc_final: 0.5790 (ttpt) REVERT: D 205 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6348 (tm-30) outliers start: 13 outliers final: 11 residues processed: 72 average time/residue: 0.5079 time to fit residues: 39.1877 Evaluate side-chains 75 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 330 VAL 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 193 THR Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 30 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.205351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.173077 restraints weight = 6489.848| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 1.90 r_work: 0.3930 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 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 : 0.003 0.040 7046 Z= 0.143 Angle : 0.556 7.585 9606 Z= 0.287 Chirality : 0.042 0.137 1071 Planarity : 0.005 0.050 1268 Dihedral : 4.133 16.189 990 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.89 % Favored : 96.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.28), residues: 874 helix: 1.87 (0.28), residues: 343 sheet: 0.15 (0.36), residues: 202 loop : -0.71 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 152 TYR 0.013 0.002 TYR D 257 PHE 0.022 0.002 PHE D 241 TRP 0.010 0.002 TRP C 120 HIS 0.003 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7046) covalent geometry : angle 0.55601 ( 9606) hydrogen bonds : bond 0.04060 ( 344) hydrogen bonds : angle 4.48212 ( 999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.33 seconds wall clock time: 45 minutes 40.59 seconds (2740.59 seconds total)