Starting phenix.real_space_refine on Sat Dec 28 23:28:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cui_27000/12_2024/8cui_27000.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cui_27000/12_2024/8cui_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_27000/12_2024/8cui_27000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cui_27000/12_2024/8cui_27000.map" model { file = "/net/cci-nas-00/data/ceres_data/8cui_27000/12_2024/8cui_27000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cui_27000/12_2024/8cui_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.74, per 1000 atoms: 0.61 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 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: 0.87 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: 2.66 Time building geometry restraints manager: 2.70 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.890 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 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:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.280 ------------------------------------------------------------------------------- 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 : 1.003 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: 1.3320 time to fit residues: 195.3456 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 : 1.032 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 1.033 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7750 (tt0) cc_final: 0.6976 (tp-100) REVERT: A 437 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7780 (tt) REVERT: B 37 LEU cc_start: 0.7933 (tp) cc_final: 0.7640 (mp) REVERT: B 200 TYR cc_start: 0.7813 (m-80) cc_final: 0.7594 (m-80) REVERT: B 205 MET cc_start: 0.8694 (ptm) cc_final: 0.8471 (ptp) REVERT: B 248 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.6958 (mpp) REVERT: B 252 GLN cc_start: 0.7825 (tt0) cc_final: 0.7025 (tp-100) REVERT: B 269 CYS cc_start: 0.7466 (m) cc_final: 0.7054 (p) REVERT: B 419 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6671 (ttt) REVERT: B 473 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8458 (mtt) REVERT: C 252 GLN cc_start: 0.7710 (tt0) cc_final: 0.6882 (tp-100) REVERT: C 473 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8452 (mtp) outliers start: 25 outliers final: 7 residues processed: 146 average time/residue: 1.1879 time to fit residues: 186.3796 Evaluate side-chains 141 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 B residue 473 MET 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 62 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 110 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9495 Z= 0.195 Angle : 0.528 8.313 12888 Z= 0.282 Chirality : 0.038 0.170 1635 Planarity : 0.004 0.034 1572 Dihedral : 3.667 14.828 1290 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.13 % Allowed : 19.55 % Favored : 77.32 % 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: 1.88 (0.16), residues: 978 sheet: 0.27 (0.62), residues: 54 loop : -2.00 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 PHE 0.015 0.002 PHE C 240 TYR 0.009 0.001 TYR A 98 ARG 0.003 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 170 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 437 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7915 (tt) REVERT: B 37 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7572 (mp) REVERT: B 205 MET cc_start: 0.8743 (ptm) cc_final: 0.8501 (ptp) REVERT: B 248 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7054 (mpp) REVERT: B 252 GLN cc_start: 0.7910 (tt0) cc_final: 0.7072 (tp-100) REVERT: B 269 CYS cc_start: 0.7573 (m) cc_final: 0.7132 (p) REVERT: B 329 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.6887 (mpp) REVERT: B 419 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6747 (ttt) REVERT: C 269 CYS cc_start: 0.7384 (m) cc_final: 0.7111 (p) REVERT: C 473 MET cc_start: 0.8739 (mtt) cc_final: 0.8488 (mtp) outliers start: 32 outliers final: 11 residues processed: 149 average time/residue: 1.1773 time to fit residues: 188.1695 Evaluate side-chains 152 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 437 ILE 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 110 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 112 optimal weight: 0.4980 chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9495 Z= 0.186 Angle : 0.527 8.212 12888 Z= 0.277 Chirality : 0.038 0.173 1635 Planarity : 0.004 0.034 1572 Dihedral : 3.681 14.906 1290 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.83 % Allowed : 19.84 % Favored : 77.32 % 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: 1.82 (0.16), residues: 978 sheet: 0.02 (0.60), residues: 54 loop : -2.04 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 19 HIS 0.002 0.001 HIS B 41 PHE 0.013 0.002 PHE A 240 TYR 0.009 0.001 TYR A 98 ARG 0.003 0.000 ARG B 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 168 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 437 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7963 (tt) REVERT: B 37 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7719 (mt) REVERT: B 205 MET cc_start: 0.8748 (ptm) cc_final: 0.8509 (ptp) REVERT: B 248 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7055 (mpp) REVERT: B 252 GLN cc_start: 0.7867 (tt0) cc_final: 0.7032 (tp-100) REVERT: B 269 CYS cc_start: 0.7554 (m) cc_final: 0.7115 (p) REVERT: B 322 GLN cc_start: 0.7711 (tt0) cc_final: 0.6856 (mt0) REVERT: B 329 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.6873 (mpp) REVERT: B 419 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6710 (ttt) REVERT: C 241 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8316 (m110) REVERT: C 269 CYS cc_start: 0.7345 (m) cc_final: 0.7090 (p) REVERT: C 322 GLN cc_start: 0.7699 (tt0) cc_final: 0.6778 (mp10) REVERT: C 473 MET cc_start: 0.8688 (mtt) cc_final: 0.8477 (mtp) outliers start: 29 outliers final: 15 residues processed: 145 average time/residue: 1.1937 time to fit residues: 185.6067 Evaluate side-chains 158 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 434 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 37 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 241 ASN Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1077 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= 0.178 Angle : 0.514 7.911 12888 Z= 0.273 Chirality : 0.038 0.171 1635 Planarity : 0.004 0.034 1572 Dihedral : 3.668 14.660 1290 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.03 % Allowed : 19.84 % 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: 1.76 (0.24), residues: 1212 helix: 1.82 (0.16), residues: 978 sheet: -0.07 (0.59), residues: 54 loop : -2.14 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 19 HIS 0.001 0.001 HIS B 41 PHE 0.013 0.002 PHE A 240 TYR 0.008 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 167 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 322 GLN cc_start: 0.7790 (tt0) cc_final: 0.7033 (mt0) REVERT: A 437 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7956 (tt) REVERT: B 37 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7582 (mp) REVERT: B 205 MET cc_start: 0.8757 (ptm) cc_final: 0.8523 (ptp) REVERT: B 248 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7049 (mpp) REVERT: B 252 GLN cc_start: 0.7830 (tt0) cc_final: 0.6986 (tp-100) REVERT: B 269 CYS cc_start: 0.7551 (m) cc_final: 0.7113 (p) REVERT: B 318 MET cc_start: 0.7716 (mtm) cc_final: 0.7454 (ttm) REVERT: B 322 GLN cc_start: 0.7669 (tt0) cc_final: 0.6815 (mt0) REVERT: B 329 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.6843 (mpp) REVERT: B 419 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6831 (ttt) REVERT: C 241 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8285 (m110) REVERT: C 269 CYS cc_start: 0.7331 (m) cc_final: 0.7084 (p) REVERT: C 322 GLN cc_start: 0.7713 (tt0) cc_final: 0.6833 (mp10) outliers start: 31 outliers final: 16 residues processed: 147 average time/residue: 1.1853 time to fit residues: 187.2134 Evaluate side-chains 157 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 37 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 241 ASN Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1121 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= 0.183 Angle : 0.518 8.500 12888 Z= 0.275 Chirality : 0.038 0.176 1635 Planarity : 0.004 0.034 1572 Dihedral : 3.667 14.646 1290 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.83 % Allowed : 20.14 % Favored : 77.03 % 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: 1.73 (0.24), residues: 1212 helix: 1.81 (0.16), residues: 978 sheet: -0.11 (0.59), residues: 54 loop : -2.15 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 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 166 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 322 GLN cc_start: 0.7824 (tt0) cc_final: 0.7102 (mp10) REVERT: A 437 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7936 (tt) REVERT: B 37 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7586 (mp) REVERT: B 205 MET cc_start: 0.8761 (ptm) cc_final: 0.8525 (ptp) REVERT: B 248 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7047 (mpp) REVERT: B 252 GLN cc_start: 0.7835 (tt0) cc_final: 0.6989 (tp-100) REVERT: B 269 CYS cc_start: 0.7553 (m) cc_final: 0.7115 (p) REVERT: B 318 MET cc_start: 0.7683 (mtm) cc_final: 0.7409 (ttm) REVERT: B 322 GLN cc_start: 0.7730 (tt0) cc_final: 0.6899 (mt0) REVERT: B 329 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.6842 (mpp) REVERT: B 406 ILE cc_start: 0.8551 (tt) cc_final: 0.8273 (tp) REVERT: B 419 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6879 (ttt) REVERT: C 241 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8292 (m110) REVERT: C 269 CYS cc_start: 0.7335 (m) cc_final: 0.7087 (p) REVERT: C 322 GLN cc_start: 0.7684 (tt0) cc_final: 0.6822 (mp10) REVERT: C 419 MET cc_start: 0.6665 (ttt) cc_final: 0.6287 (ttt) outliers start: 29 outliers final: 17 residues processed: 146 average time/residue: 1.2190 time to fit residues: 190.8609 Evaluate side-chains 158 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 37 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 241 ASN 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 13 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1146 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= 0.170 Angle : 0.508 8.478 12888 Z= 0.270 Chirality : 0.038 0.180 1635 Planarity : 0.004 0.034 1572 Dihedral : 3.637 14.486 1290 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.83 % Allowed : 20.72 % 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: 1.81 (0.24), residues: 1212 helix: 1.92 (0.16), residues: 963 sheet: -0.11 (0.60), residues: 54 loop : -2.11 (0.37), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 167 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 322 GLN cc_start: 0.7821 (tt0) cc_final: 0.7100 (mp10) REVERT: B 37 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7579 (mp) REVERT: B 205 MET cc_start: 0.8750 (ptm) cc_final: 0.8513 (ptp) REVERT: B 248 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7041 (mpp) REVERT: B 252 GLN cc_start: 0.7825 (tt0) cc_final: 0.6984 (tp-100) REVERT: B 269 CYS cc_start: 0.7525 (m) cc_final: 0.7090 (p) REVERT: B 318 MET cc_start: 0.7676 (mtm) cc_final: 0.7406 (ttm) REVERT: B 322 GLN cc_start: 0.7713 (tt0) cc_final: 0.6890 (mt0) REVERT: B 406 ILE cc_start: 0.8559 (tt) cc_final: 0.8280 (tp) REVERT: C 252 GLN cc_start: 0.7753 (tt0) cc_final: 0.6897 (tp-100) REVERT: C 269 CYS cc_start: 0.7342 (m) cc_final: 0.7083 (p) REVERT: C 322 GLN cc_start: 0.7689 (tt0) cc_final: 0.6840 (mp10) outliers start: 29 outliers final: 15 residues processed: 149 average time/residue: 1.1665 time to fit residues: 186.7852 Evaluate side-chains 153 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 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 115 SER Chi-restraints excluded: chain B residue 248 MET 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 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 70 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9495 Z= 0.191 Angle : 0.526 8.389 12888 Z= 0.280 Chirality : 0.038 0.185 1635 Planarity : 0.004 0.034 1572 Dihedral : 3.667 13.655 1290 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.74 % Allowed : 21.11 % Favored : 76.15 % 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: 1.67 (0.24), residues: 1212 helix: 1.77 (0.16), residues: 978 sheet: -0.17 (0.59), residues: 54 loop : -2.19 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 19 HIS 0.001 0.000 HIS C 296 PHE 0.014 0.002 PHE A 240 TYR 0.009 0.001 TYR C 98 ARG 0.006 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 165 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 286 MET cc_start: 0.7905 (mpp) cc_final: 0.7689 (mtt) REVERT: A 322 GLN cc_start: 0.7787 (tt0) cc_final: 0.7052 (mt0) REVERT: A 437 ILE cc_start: 0.8114 (tt) cc_final: 0.7880 (tt) REVERT: B 205 MET cc_start: 0.8757 (ptm) cc_final: 0.8519 (ptp) REVERT: B 248 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7060 (mpp) REVERT: B 252 GLN cc_start: 0.7896 (tt0) cc_final: 0.7056 (tp-100) REVERT: B 269 CYS cc_start: 0.7563 (m) cc_final: 0.7124 (p) REVERT: B 318 MET cc_start: 0.7701 (mtm) cc_final: 0.7413 (ttm) REVERT: B 322 GLN cc_start: 0.7725 (tt0) cc_final: 0.6915 (mt0) REVERT: B 406 ILE cc_start: 0.8554 (tt) cc_final: 0.8279 (tp) REVERT: C 241 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8312 (m110) REVERT: C 269 CYS cc_start: 0.7342 (m) cc_final: 0.7095 (p) REVERT: C 322 GLN cc_start: 0.7728 (tt0) cc_final: 0.6878 (mp10) REVERT: C 406 ILE cc_start: 0.8551 (tt) cc_final: 0.8204 (tp) REVERT: C 419 MET cc_start: 0.6687 (ttt) cc_final: 0.6414 (ttt) outliers start: 28 outliers final: 16 residues processed: 152 average time/residue: 1.1605 time to fit residues: 189.4705 Evaluate side-chains 154 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 37 LEU 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 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 241 ASN 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 103 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 116 optimal weight: 0.0370 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9495 Z= 0.179 Angle : 0.527 8.852 12888 Z= 0.278 Chirality : 0.038 0.187 1635 Planarity : 0.004 0.034 1572 Dihedral : 3.630 13.566 1290 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.05 % Allowed : 21.70 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1212 helix: 1.80 (0.16), residues: 975 sheet: -0.15 (0.60), residues: 54 loop : -2.24 (0.38), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 19 HIS 0.001 0.000 HIS C 296 PHE 0.012 0.002 PHE A 240 TYR 0.009 0.001 TYR C 98 ARG 0.007 0.000 ARG B 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 159 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 322 GLN cc_start: 0.7769 (tt0) cc_final: 0.7039 (mt0) REVERT: A 396 THR cc_start: 0.8167 (p) cc_final: 0.7949 (t) REVERT: A 437 ILE cc_start: 0.8127 (tt) cc_final: 0.7885 (tt) REVERT: B 37 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7624 (mp) REVERT: B 205 MET cc_start: 0.8751 (ptm) cc_final: 0.8514 (ptp) REVERT: B 248 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7051 (mpp) REVERT: B 252 GLN cc_start: 0.7826 (tt0) cc_final: 0.6981 (tp-100) REVERT: B 269 CYS cc_start: 0.7530 (m) cc_final: 0.7097 (p) REVERT: B 318 MET cc_start: 0.7669 (mtm) cc_final: 0.7387 (ttm) REVERT: B 322 GLN cc_start: 0.7720 (tt0) cc_final: 0.6917 (mt0) REVERT: B 406 ILE cc_start: 0.8569 (tt) cc_final: 0.8301 (tp) REVERT: B 419 MET cc_start: 0.6810 (ttt) cc_final: 0.6565 (ttt) REVERT: C 241 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8295 (m110) REVERT: C 252 GLN cc_start: 0.7737 (tt0) cc_final: 0.6882 (tp-100) REVERT: C 269 CYS cc_start: 0.7349 (m) cc_final: 0.7091 (p) REVERT: C 322 GLN cc_start: 0.7721 (tt0) cc_final: 0.6872 (mp10) REVERT: C 406 ILE cc_start: 0.8525 (tt) cc_final: 0.8175 (tp) REVERT: C 419 MET cc_start: 0.6690 (ttt) cc_final: 0.6371 (ttt) outliers start: 21 outliers final: 14 residues processed: 147 average time/residue: 1.2124 time to fit residues: 191.3206 Evaluate side-chains 155 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 272 GLU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 37 LEU 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 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 241 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.0470 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9495 Z= 0.166 Angle : 0.519 8.745 12888 Z= 0.273 Chirality : 0.038 0.184 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.589 14.255 1290 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.86 % Allowed : 21.70 % 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: 1.82 (0.24), residues: 1212 helix: 1.93 (0.16), residues: 963 sheet: -0.11 (0.60), residues: 54 loop : -2.15 (0.36), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 19 HIS 0.001 0.000 HIS C 296 PHE 0.011 0.001 PHE A 240 TYR 0.008 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 160 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7790 (tt0) cc_final: 0.7003 (tp-100) REVERT: A 322 GLN cc_start: 0.7785 (tt0) cc_final: 0.7054 (mt0) REVERT: A 396 THR cc_start: 0.8171 (p) cc_final: 0.7964 (t) REVERT: A 437 ILE cc_start: 0.8191 (tt) cc_final: 0.7958 (tt) REVERT: B 37 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7666 (mp) REVERT: B 205 MET cc_start: 0.8752 (ptm) cc_final: 0.8517 (ptp) REVERT: B 248 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7032 (mpp) REVERT: B 252 GLN cc_start: 0.7833 (tt0) cc_final: 0.6998 (tp-100) REVERT: B 269 CYS cc_start: 0.7499 (m) cc_final: 0.7077 (p) REVERT: B 318 MET cc_start: 0.7664 (mtm) cc_final: 0.7412 (ttm) REVERT: B 322 GLN cc_start: 0.7665 (tt0) cc_final: 0.6824 (mt0) REVERT: B 406 ILE cc_start: 0.8532 (tt) cc_final: 0.8271 (tp) REVERT: B 419 MET cc_start: 0.6826 (ttt) cc_final: 0.6559 (ttt) REVERT: C 252 GLN cc_start: 0.7736 (tt0) cc_final: 0.6885 (tp-100) REVERT: C 269 CYS cc_start: 0.7302 (m) cc_final: 0.7056 (p) REVERT: C 322 GLN cc_start: 0.7690 (tt0) cc_final: 0.6835 (mp10) REVERT: C 406 ILE cc_start: 0.8524 (tt) cc_final: 0.8181 (tp) REVERT: C 419 MET cc_start: 0.6713 (ttt) cc_final: 0.6328 (ttt) outliers start: 19 outliers final: 14 residues processed: 148 average time/residue: 1.2128 time to fit residues: 193.0373 Evaluate side-chains 154 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 272 GLU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 37 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 100 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.157935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112301 restraints weight = 9815.650| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.88 r_work: 0.3126 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9495 Z= 0.145 Angle : 0.496 8.698 12888 Z= 0.259 Chirality : 0.037 0.177 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.514 13.268 1290 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.76 % Allowed : 21.90 % 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: 1.83 (0.24), residues: 1212 helix: 1.94 (0.16), residues: 981 sheet: -0.03 (0.61), residues: 54 loop : -2.64 (0.34), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 19 HIS 0.001 0.000 HIS A 296 PHE 0.010 0.001 PHE B 99 TYR 0.008 0.001 TYR A 285 ARG 0.006 0.000 ARG A 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3544.17 seconds wall clock time: 64 minutes 8.50 seconds (3848.50 seconds total)