Starting phenix.real_space_refine on Thu Feb 13 20:06:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cui_27000/02_2025/8cui_27000.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cui_27000/02_2025/8cui_27000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cui_27000/02_2025/8cui_27000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cui_27000/02_2025/8cui_27000.map" model { file = "/net/cci-nas-00/data/ceres_data/8cui_27000/02_2025/8cui_27000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cui_27000/02_2025/8cui_27000.cif" } resolution = 2.55 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= 0.008 sd= 0.102 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 63 5.16 5 C 6132 2.51 5 N 1491 2.21 5 O 1671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9357 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3119 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 11, 'TRANS': 398} Chain breaks: 2 Restraints were copied for chains: C, B Time building chain proxies: 6.12, per 1000 atoms: 0.65 Number of scatterers: 9357 At special positions: 0 Unit cell: (108.204, 103.944, 75.828, 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 63 16.00 O 1671 8.00 N 1491 7.00 C 6132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 441 " distance=2.95 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 84.6% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.678A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.624A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 81 removed outlier: 3.553A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.598A pdb=" N ILE A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.546A pdb=" N MET A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.743A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 removed outlier: 3.772A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.790A pdb=" N VAL A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 284 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.860A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 removed outlier: 4.126A pdb=" N ALA A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 405 removed outlier: 3.967A pdb=" N SER A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 429 through 436 removed outlier: 4.165A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.942A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 474 removed outlier: 3.778A pdb=" N ASP A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 42 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.679A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.624A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 81 removed outlier: 3.553A pdb=" N LEU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 117 removed outlier: 3.598A pdb=" N ILE B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.547A pdb=" N MET B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 230 removed outlier: 3.743A pdb=" N GLY B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 removed outlier: 3.772A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.790A pdb=" N VAL B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.860A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 351 through 366 Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 385 removed outlier: 4.125A pdb=" N ALA B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 405 removed outlier: 3.967A pdb=" N SER B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.165A pdb=" N ASP B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 433 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR B 434 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.942A pdb=" N ARG B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 474 removed outlier: 3.778A pdb=" N ASP B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 42 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.677A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 66 removed outlier: 3.624A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 81 removed outlier: 3.553A pdb=" N LEU C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 117 removed outlier: 3.598A pdb=" N ILE C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.546A pdb=" N MET C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 230 removed outlier: 3.744A pdb=" N GLY C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 removed outlier: 3.772A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.790A pdb=" N VAL C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 284 through 299 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.860A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 351 through 366 Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 367 through 385 removed outlier: 4.126A pdb=" N ALA C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 removed outlier: 3.966A pdb=" N SER C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 426 Processing helix chain 'C' and resid 429 through 436 removed outlier: 4.164A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL C 433 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR C 434 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.942A pdb=" N ARG C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 474 removed outlier: 3.778A pdb=" N ASP C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167 732 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 2.91 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: 2925 1.34 - 1.46: 1778 1.46 - 1.58: 4675 1.58 - 1.70: 0 1.70 - 1.81: 117 Bond restraints: 9495 Sorted by residual: bond pdb=" N CYS B 269 " pdb=" CA CYS B 269 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.38e+00 bond pdb=" N CYS B 441 " pdb=" CA CYS B 441 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.33e+00 bond pdb=" N CYS A 441 " pdb=" CA CYS A 441 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.32e+00 bond pdb=" N CYS A 269 " pdb=" CA CYS A 269 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.95e+00 bond pdb=" N CYS C 441 " pdb=" CA CYS C 441 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 4.90e+00 ... (remaining 9490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 12679 1.71 - 3.42: 173 3.42 - 5.13: 30 5.13 - 6.84: 3 6.84 - 8.55: 3 Bond angle restraints: 12888 Sorted by residual: angle pdb=" CA CYS A 441 " pdb=" C CYS A 441 " pdb=" O CYS A 441 " ideal model delta sigma weight residual 120.90 118.22 2.68 1.07e+00 8.73e-01 6.27e+00 angle pdb=" CA CYS B 441 " pdb=" C CYS B 441 " pdb=" O CYS B 441 " ideal model delta sigma weight residual 120.82 118.20 2.62 1.05e+00 9.07e-01 6.23e+00 angle pdb=" CA CYS C 441 " pdb=" C CYS C 441 " pdb=" O CYS C 441 " ideal model delta sigma weight residual 120.90 118.25 2.65 1.07e+00 8.73e-01 6.13e+00 angle pdb=" CA LEU B 416 " pdb=" CB LEU B 416 " pdb=" CG LEU B 416 " ideal model delta sigma weight residual 116.30 124.85 -8.55 3.50e+00 8.16e-02 5.96e+00 angle pdb=" CA LEU C 416 " pdb=" CB LEU C 416 " pdb=" CG LEU C 416 " ideal model delta sigma weight residual 116.30 124.82 -8.52 3.50e+00 8.16e-02 5.93e+00 ... (remaining 12883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5026 17.90 - 35.79: 478 35.79 - 53.69: 147 53.69 - 71.58: 19 71.58 - 89.48: 9 Dihedral angle restraints: 5679 sinusoidal: 2154 harmonic: 3525 Sorted by residual: dihedral pdb=" CB CYS A 269 " pdb=" SG CYS A 269 " pdb=" SG CYS A 441 " pdb=" CB CYS A 441 " ideal model delta sinusoidal sigma weight residual -86.00 -17.12 -68.88 1 1.00e+01 1.00e-02 6.14e+01 dihedral pdb=" CB GLU B 471 " pdb=" CG GLU B 471 " pdb=" CD GLU B 471 " pdb=" OE1 GLU B 471 " ideal model delta sinusoidal sigma weight residual 0.00 -89.48 89.48 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 471 " pdb=" CG GLU A 471 " pdb=" CD GLU A 471 " pdb=" OE1 GLU A 471 " ideal model delta sinusoidal sigma weight residual 0.00 -89.42 89.42 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1164 0.034 - 0.069: 355 0.069 - 0.103: 90 0.103 - 0.137: 22 0.137 - 0.172: 4 Chirality restraints: 1635 Sorted by residual: chirality pdb=" CA CYS B 441 " pdb=" N CYS B 441 " pdb=" C CYS B 441 " pdb=" CB CYS B 441 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA CYS A 441 " pdb=" N CYS A 441 " pdb=" C CYS A 441 " pdb=" CB CYS A 441 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA CYS C 441 " pdb=" N CYS C 441 " pdb=" C CYS C 441 " pdb=" CB CYS C 441 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 1632 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 295 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C ILE C 295 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE C 295 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS C 296 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 295 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C ILE A 295 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 295 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS A 296 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 295 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C ILE B 295 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE B 295 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS B 296 " 0.010 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2140 2.79 - 3.32: 9135 3.32 - 3.85: 15324 3.85 - 4.37: 17103 4.37 - 4.90: 31052 Nonbonded interactions: 74754 Sorted by model distance: nonbonded pdb=" O GLY B 392 " pdb=" OG1 THR B 396 " model vdw 2.264 3.040 nonbonded pdb=" O GLY A 392 " pdb=" OG1 THR A 396 " model vdw 2.265 3.040 nonbonded pdb=" O GLY C 392 " pdb=" OG1 THR C 396 " model vdw 2.265 3.040 nonbonded pdb=" O VAL C 20 " pdb=" OG1 THR C 24 " model vdw 2.316 3.040 nonbonded pdb=" O VAL B 20 " pdb=" OG1 THR B 24 " model vdw 2.316 3.040 ... (remaining 74749 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.500 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 24.400 Find NCS groups from input model: 0.180 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.003 0.028 9495 Z= 0.177 Angle : 0.534 8.546 12888 Z= 0.299 Chirality : 0.037 0.172 1635 Planarity : 0.004 0.030 1572 Dihedral : 15.717 89.480 3402 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 22.87 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.24), residues: 1212 helix: 1.71 (0.16), residues: 978 sheet: 0.95 (0.68), residues: 54 loop : -1.99 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 19 HIS 0.001 0.000 HIS B 296 PHE 0.009 0.001 PHE A 240 TYR 0.009 0.001 TYR A 98 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.036 Fit side-chains REVERT: A 252 GLN cc_start: 0.7831 (tt0) cc_final: 0.7048 (tp-100) REVERT: B 37 LEU cc_start: 0.7938 (tp) cc_final: 0.7658 (mp) REVERT: B 165 LYS cc_start: 0.7957 (ptpp) cc_final: 0.7669 (ptpt) REVERT: B 200 TYR cc_start: 0.7839 (m-80) cc_final: 0.7567 (m-80) REVERT: B 205 MET cc_start: 0.8755 (ptm) cc_final: 0.8494 (ptp) REVERT: B 252 GLN cc_start: 0.7788 (tt0) cc_final: 0.7023 (tp-100) REVERT: C 252 GLN cc_start: 0.7726 (tt0) cc_final: 0.6925 (tp-100) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 1.3030 time to fit residues: 190.9077 Evaluate side-chains 130 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.0670 chunk 111 optimal weight: 3.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.158351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113132 restraints weight = 9761.667| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.87 r_work: 0.3141 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9495 Z= 0.141 Angle : 0.481 7.688 12888 Z= 0.256 Chirality : 0.037 0.132 1635 Planarity : 0.004 0.032 1572 Dihedral : 3.537 13.583 1290 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.44 % Allowed : 21.11 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.24), residues: 1212 helix: 1.95 (0.16), residues: 990 sheet: 0.64 (0.65), residues: 54 loop : -2.57 (0.37), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 19 HIS 0.001 0.000 HIS B 296 PHE 0.009 0.001 PHE C 239 TYR 0.007 0.001 TYR B 98 ARG 0.004 0.000 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7998 (tt0) cc_final: 0.7068 (tp-100) REVERT: A 437 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7484 (tt) REVERT: B 37 LEU cc_start: 0.7609 (tp) cc_final: 0.7341 (mp) REVERT: B 200 TYR cc_start: 0.7809 (m-80) cc_final: 0.7574 (m-80) REVERT: B 205 MET cc_start: 0.8975 (ptm) cc_final: 0.8725 (ptp) REVERT: B 248 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7379 (mpp) REVERT: B 252 GLN cc_start: 0.8050 (tt0) cc_final: 0.7072 (tp-100) REVERT: B 269 CYS cc_start: 0.7666 (m) cc_final: 0.6898 (p) REVERT: B 419 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6780 (ttt) REVERT: C 252 GLN cc_start: 0.7932 (tt0) cc_final: 0.6985 (tp-100) REVERT: C 473 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8165 (mtp) outliers start: 25 outliers final: 7 residues processed: 146 average time/residue: 1.1767 time to fit residues: 184.5433 Evaluate side-chains 140 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 473 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 2 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109048 restraints weight = 9831.121| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.90 r_work: 0.3083 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9495 Z= 0.174 Angle : 0.509 8.400 12888 Z= 0.271 Chirality : 0.038 0.170 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.609 14.901 1290 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.93 % Allowed : 19.94 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.24), residues: 1212 helix: 1.96 (0.16), residues: 975 sheet: 0.29 (0.62), residues: 54 loop : -1.98 (0.39), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 19 HIS 0.001 0.000 HIS B 296 PHE 0.013 0.002 PHE C 240 TYR 0.008 0.001 TYR A 98 ARG 0.004 0.000 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: B 37 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7308 (mp) REVERT: B 205 MET cc_start: 0.9020 (ptm) cc_final: 0.8753 (ptp) REVERT: B 248 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.7497 (mpp) REVERT: B 252 GLN cc_start: 0.8078 (tt0) cc_final: 0.7067 (tp-100) REVERT: B 269 CYS cc_start: 0.7742 (m) cc_final: 0.6951 (p) REVERT: B 329 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.6745 (mpp) REVERT: B 419 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6851 (ttt) REVERT: C 269 CYS cc_start: 0.7514 (m) cc_final: 0.6934 (p) REVERT: C 473 MET cc_start: 0.8426 (mtt) cc_final: 0.8129 (mtp) outliers start: 30 outliers final: 12 residues processed: 145 average time/residue: 1.1642 time to fit residues: 181.0358 Evaluate side-chains 149 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 351 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 81 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.154411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108280 restraints weight = 9834.791| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.89 r_work: 0.3073 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9495 Z= 0.184 Angle : 0.526 8.196 12888 Z= 0.276 Chirality : 0.038 0.182 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.653 14.856 1290 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.64 % Allowed : 19.84 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.24), residues: 1212 helix: 1.85 (0.16), residues: 978 sheet: 0.04 (0.60), residues: 54 loop : -2.03 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 19 HIS 0.001 0.000 HIS C 296 PHE 0.013 0.002 PHE A 240 TYR 0.009 0.001 TYR A 98 ARG 0.003 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 437 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7673 (tt) REVERT: A 473 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8156 (mtt) REVERT: B 205 MET cc_start: 0.9037 (ptm) cc_final: 0.8774 (ptp) REVERT: B 248 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.7515 (mpp) REVERT: B 252 GLN cc_start: 0.8123 (tt0) cc_final: 0.7117 (tp-100) REVERT: B 269 CYS cc_start: 0.7769 (m) cc_final: 0.6976 (p) REVERT: B 322 GLN cc_start: 0.7719 (tt0) cc_final: 0.6702 (mt0) REVERT: B 329 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.6730 (mpp) REVERT: B 419 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6808 (ttt) REVERT: C 269 CYS cc_start: 0.7499 (m) cc_final: 0.6939 (p) REVERT: C 473 MET cc_start: 0.8410 (mtt) cc_final: 0.8164 (mtp) outliers start: 27 outliers final: 13 residues processed: 144 average time/residue: 1.2501 time to fit residues: 192.9233 Evaluate side-chains 152 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 351 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 51 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN C 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.156542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110776 restraints weight = 9834.178| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.88 r_work: 0.3106 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9495 Z= 0.153 Angle : 0.491 7.897 12888 Z= 0.259 Chirality : 0.037 0.168 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.579 14.580 1290 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.35 % Allowed : 20.92 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.24), residues: 1212 helix: 1.86 (0.16), residues: 993 sheet: 0.02 (0.61), residues: 54 loop : -2.67 (0.37), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 19 HIS 0.002 0.000 HIS B 41 PHE 0.010 0.001 PHE C 240 TYR 0.007 0.001 TYR C 98 ARG 0.003 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.8015 (tt0) cc_final: 0.7079 (tp-100) REVERT: A 322 GLN cc_start: 0.7798 (tt0) cc_final: 0.6925 (mt0) REVERT: A 437 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7640 (tt) REVERT: A 473 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8115 (mtt) REVERT: B 205 MET cc_start: 0.9033 (ptm) cc_final: 0.8775 (ptp) REVERT: B 248 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.7509 (mpp) REVERT: B 252 GLN cc_start: 0.8065 (tt0) cc_final: 0.7070 (tp-100) REVERT: B 269 CYS cc_start: 0.7722 (m) cc_final: 0.6949 (p) REVERT: B 322 GLN cc_start: 0.7644 (tt0) cc_final: 0.6634 (mt0) REVERT: B 329 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.6597 (mpp) REVERT: B 419 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6910 (ttt) REVERT: C 252 GLN cc_start: 0.7967 (tt0) cc_final: 0.6989 (tp-100) REVERT: C 269 CYS cc_start: 0.7466 (m) cc_final: 0.6911 (p) REVERT: C 322 GLN cc_start: 0.7689 (tt0) cc_final: 0.6692 (mp10) REVERT: C 473 MET cc_start: 0.8360 (mtt) cc_final: 0.8149 (mtp) outliers start: 24 outliers final: 12 residues processed: 145 average time/residue: 1.2075 time to fit residues: 189.0343 Evaluate side-chains 150 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 351 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 0.0050 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.155362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109281 restraints weight = 9847.932| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.90 r_work: 0.3086 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9495 Z= 0.171 Angle : 0.507 8.304 12888 Z= 0.268 Chirality : 0.038 0.175 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.598 14.493 1290 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.64 % Allowed : 20.43 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.24), residues: 1212 helix: 1.90 (0.16), residues: 975 sheet: -0.03 (0.60), residues: 54 loop : -2.13 (0.38), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 19 HIS 0.001 0.000 HIS C 296 PHE 0.013 0.001 PHE C 240 TYR 0.008 0.001 TYR C 98 ARG 0.003 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7802 (mtm) cc_final: 0.7580 (ttm) REVERT: A 322 GLN cc_start: 0.7898 (tt0) cc_final: 0.7022 (mt0) REVERT: A 437 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7670 (tt) REVERT: A 473 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8107 (mtt) REVERT: B 205 MET cc_start: 0.9032 (ptm) cc_final: 0.8772 (ptp) REVERT: B 248 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.7512 (mpp) REVERT: B 252 GLN cc_start: 0.8069 (tt0) cc_final: 0.7056 (tp-100) REVERT: B 269 CYS cc_start: 0.7741 (m) cc_final: 0.6961 (p) REVERT: B 318 MET cc_start: 0.7751 (mtm) cc_final: 0.7436 (ttm) REVERT: B 322 GLN cc_start: 0.7726 (tt0) cc_final: 0.6756 (mt0) REVERT: B 406 ILE cc_start: 0.8380 (tt) cc_final: 0.8030 (tp) REVERT: B 419 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6983 (ttt) REVERT: C 269 CYS cc_start: 0.7506 (m) cc_final: 0.6940 (p) REVERT: C 322 GLN cc_start: 0.7702 (tt0) cc_final: 0.6689 (mp10) REVERT: C 473 MET cc_start: 0.8379 (mtt) cc_final: 0.8169 (mtp) outliers start: 27 outliers final: 14 residues processed: 147 average time/residue: 1.1793 time to fit residues: 186.2342 Evaluate side-chains 152 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 102 optimal weight: 0.7980 chunk 100 optimal weight: 0.0770 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.155393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109380 restraints weight = 9864.653| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.90 r_work: 0.3084 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9495 Z= 0.172 Angle : 0.509 8.200 12888 Z= 0.270 Chirality : 0.038 0.179 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.598 14.292 1290 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.96 % Allowed : 20.92 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.24), residues: 1212 helix: 1.94 (0.16), residues: 963 sheet: -0.06 (0.60), residues: 54 loop : -2.09 (0.37), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 19 HIS 0.001 0.000 HIS C 296 PHE 0.012 0.001 PHE A 240 TYR 0.008 0.001 TYR C 98 ARG 0.003 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7786 (mtm) cc_final: 0.7550 (ttm) REVERT: A 322 GLN cc_start: 0.7897 (tt0) cc_final: 0.7026 (mt0) REVERT: A 473 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8113 (mtt) REVERT: B 205 MET cc_start: 0.9036 (ptm) cc_final: 0.8775 (ptp) REVERT: B 248 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.7505 (mpp) REVERT: B 252 GLN cc_start: 0.8084 (tt0) cc_final: 0.7072 (tp-100) REVERT: B 269 CYS cc_start: 0.7736 (m) cc_final: 0.6955 (p) REVERT: B 318 MET cc_start: 0.7754 (mtm) cc_final: 0.7438 (ttm) REVERT: B 322 GLN cc_start: 0.7677 (tt0) cc_final: 0.6685 (mt0) REVERT: B 406 ILE cc_start: 0.8360 (tt) cc_final: 0.8012 (tp) REVERT: B 419 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.7021 (ttt) REVERT: C 252 GLN cc_start: 0.7978 (tt0) cc_final: 0.6994 (tp-100) REVERT: C 269 CYS cc_start: 0.7486 (m) cc_final: 0.6924 (p) REVERT: C 322 GLN cc_start: 0.7716 (tt0) cc_final: 0.6707 (mp10) REVERT: C 406 ILE cc_start: 0.8269 (tt) cc_final: 0.7825 (tp) REVERT: C 473 MET cc_start: 0.8387 (mtt) cc_final: 0.8174 (mtp) outliers start: 20 outliers final: 12 residues processed: 144 average time/residue: 1.2137 time to fit residues: 187.2212 Evaluate side-chains 151 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.156143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110224 restraints weight = 9887.809| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.89 r_work: 0.3102 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9495 Z= 0.161 Angle : 0.497 8.193 12888 Z= 0.264 Chirality : 0.038 0.182 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.545 13.393 1290 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.86 % Allowed : 21.31 % Favored : 76.83 % 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: 1.90 (0.24), residues: 1212 helix: 1.98 (0.16), residues: 963 sheet: -0.04 (0.60), residues: 54 loop : -2.07 (0.37), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 19 HIS 0.001 0.000 HIS C 296 PHE 0.011 0.001 PHE C 240 TYR 0.008 0.001 TYR C 98 ARG 0.004 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7759 (mtm) cc_final: 0.7529 (ttm) REVERT: A 322 GLN cc_start: 0.7864 (tt0) cc_final: 0.6986 (mt0) REVERT: A 406 ILE cc_start: 0.8298 (tt) cc_final: 0.8025 (tp) REVERT: A 437 ILE cc_start: 0.7843 (tt) cc_final: 0.7616 (tt) REVERT: B 205 MET cc_start: 0.9035 (ptm) cc_final: 0.8778 (ptp) REVERT: B 248 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7487 (mpp) REVERT: B 252 GLN cc_start: 0.8071 (tt0) cc_final: 0.7065 (tp-100) REVERT: B 269 CYS cc_start: 0.7728 (m) cc_final: 0.6953 (p) REVERT: B 318 MET cc_start: 0.7669 (mtm) cc_final: 0.7362 (ttm) REVERT: B 320 MET cc_start: 0.8477 (mmm) cc_final: 0.8174 (mmm) REVERT: B 322 GLN cc_start: 0.7672 (tt0) cc_final: 0.6667 (mt0) REVERT: B 406 ILE cc_start: 0.8355 (tt) cc_final: 0.8016 (tp) REVERT: B 419 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.7029 (ttt) REVERT: C 252 GLN cc_start: 0.7979 (tt0) cc_final: 0.7001 (tp-100) REVERT: C 269 CYS cc_start: 0.7465 (m) cc_final: 0.6915 (p) REVERT: C 322 GLN cc_start: 0.7701 (tt0) cc_final: 0.6675 (mp10) REVERT: C 406 ILE cc_start: 0.8280 (tt) cc_final: 0.7839 (tp) REVERT: C 473 MET cc_start: 0.8354 (mtt) cc_final: 0.8134 (mtp) outliers start: 19 outliers final: 12 residues processed: 147 average time/residue: 1.1832 time to fit residues: 186.4431 Evaluate side-chains 152 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 86 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 34 optimal weight: 0.0670 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 0.0000 chunk 69 optimal weight: 4.9990 overall best weight: 0.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.113265 restraints weight = 9815.581| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.87 r_work: 0.3141 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9495 Z= 0.140 Angle : 0.478 8.214 12888 Z= 0.253 Chirality : 0.037 0.129 1635 Planarity : 0.003 0.033 1572 Dihedral : 3.467 13.151 1290 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.86 % Allowed : 21.41 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.24), residues: 1212 helix: 1.97 (0.16), residues: 981 sheet: 0.03 (0.61), residues: 54 loop : -2.56 (0.35), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 19 HIS 0.001 0.000 HIS C 296 PHE 0.009 0.001 PHE C 239 TYR 0.007 0.001 TYR C 98 ARG 0.007 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7998 (tt0) cc_final: 0.7070 (tp-100) REVERT: A 312 ASN cc_start: 0.8169 (t0) cc_final: 0.7771 (t0) REVERT: A 318 MET cc_start: 0.7679 (mtm) cc_final: 0.7444 (ttm) REVERT: A 322 GLN cc_start: 0.7805 (tt0) cc_final: 0.6913 (mt0) REVERT: A 406 ILE cc_start: 0.8280 (tt) cc_final: 0.7999 (tp) REVERT: A 437 ILE cc_start: 0.7862 (tt) cc_final: 0.7633 (tt) REVERT: B 205 MET cc_start: 0.9012 (ptm) cc_final: 0.8780 (ptp) REVERT: B 248 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7421 (mpp) REVERT: B 252 GLN cc_start: 0.8027 (tt0) cc_final: 0.7053 (tp-100) REVERT: B 269 CYS cc_start: 0.7650 (m) cc_final: 0.6884 (p) REVERT: B 318 MET cc_start: 0.7645 (mtm) cc_final: 0.7358 (ttm) REVERT: B 322 GLN cc_start: 0.7601 (tt0) cc_final: 0.6611 (mt0) REVERT: B 406 ILE cc_start: 0.8334 (tt) cc_final: 0.8008 (tp) REVERT: C 252 GLN cc_start: 0.7873 (tt0) cc_final: 0.6925 (tp-100) REVERT: C 269 CYS cc_start: 0.7381 (m) cc_final: 0.6843 (p) REVERT: C 322 GLN cc_start: 0.7625 (tt0) cc_final: 0.6612 (mp10) REVERT: C 406 ILE cc_start: 0.8250 (tt) cc_final: 0.7820 (tp) outliers start: 19 outliers final: 13 residues processed: 151 average time/residue: 1.1406 time to fit residues: 185.2989 Evaluate side-chains 153 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.155369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109058 restraints weight = 9878.773| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.91 r_work: 0.3079 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9495 Z= 0.184 Angle : 0.523 8.370 12888 Z= 0.276 Chirality : 0.038 0.131 1635 Planarity : 0.004 0.034 1572 Dihedral : 3.565 13.553 1290 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.47 % Allowed : 21.99 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.24), residues: 1212 helix: 1.89 (0.16), residues: 975 sheet: -0.13 (0.60), residues: 54 loop : -2.15 (0.38), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 19 HIS 0.001 0.000 HIS B 296 PHE 0.013 0.002 PHE A 240 TYR 0.009 0.001 TYR C 98 ARG 0.006 0.000 ARG A 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8252 (mmp) cc_final: 0.8038 (mmm) REVERT: A 318 MET cc_start: 0.7816 (mtm) cc_final: 0.7578 (ttm) REVERT: A 322 GLN cc_start: 0.7871 (tt0) cc_final: 0.7008 (mt0) REVERT: A 406 ILE cc_start: 0.8296 (tt) cc_final: 0.8022 (tp) REVERT: A 437 ILE cc_start: 0.7903 (tt) cc_final: 0.7677 (tt) REVERT: B 205 MET cc_start: 0.9040 (ptm) cc_final: 0.8779 (ptp) REVERT: B 248 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7523 (mpp) REVERT: B 252 GLN cc_start: 0.8125 (tt0) cc_final: 0.7148 (tp-100) REVERT: B 269 CYS cc_start: 0.7757 (m) cc_final: 0.6978 (p) REVERT: B 318 MET cc_start: 0.7746 (mtm) cc_final: 0.7438 (ttm) REVERT: B 322 GLN cc_start: 0.7659 (tt0) cc_final: 0.6672 (mt0) REVERT: B 406 ILE cc_start: 0.8350 (tt) cc_final: 0.8023 (tp) REVERT: C 269 CYS cc_start: 0.7477 (m) cc_final: 0.6915 (p) REVERT: C 322 GLN cc_start: 0.7705 (tt0) cc_final: 0.6712 (mp10) REVERT: C 406 ILE cc_start: 0.8280 (tt) cc_final: 0.7844 (tp) REVERT: C 419 MET cc_start: 0.6827 (ttt) cc_final: 0.6543 (ttt) outliers start: 15 outliers final: 12 residues processed: 146 average time/residue: 1.2143 time to fit residues: 190.1831 Evaluate side-chains 150 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103550 restraints weight = 9812.383| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.90 r_work: 0.3003 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9495 Z= 0.336 Angle : 0.644 8.337 12888 Z= 0.342 Chirality : 0.043 0.154 1635 Planarity : 0.005 0.043 1572 Dihedral : 3.935 14.236 1290 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.47 % Allowed : 22.19 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.23), residues: 1212 helix: 1.51 (0.16), residues: 969 sheet: 0.56 (0.49), residues: 48 loop : -2.79 (0.36), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 256 HIS 0.003 0.001 HIS B 296 PHE 0.022 0.003 PHE A 240 TYR 0.012 0.002 TYR A 98 ARG 0.006 0.001 ARG A 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7460.10 seconds wall clock time: 131 minutes 47.09 seconds (7907.09 seconds total)