Starting phenix.real_space_refine on Thu Mar 14 17:32:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cui_27000/03_2024/8cui_27000.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cui_27000/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cui_27000/03_2024/8cui_27000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cui_27000/03_2024/8cui_27000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cui_27000/03_2024/8cui_27000.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cui_27000/03_2024/8cui_27000.pdb" } 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 Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B ASP 368": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C GLU 471": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9357 Number of models: 1 Model: "" Number of chains: 3 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 Chain: "B" 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 Chain: "C" 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 Time building chain proxies: 5.36, per 1000 atoms: 0.57 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=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 441 " distance=2.95 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 441 " distance=2.95 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 441 " distance=2.95 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.38 Conformation dependent library (CDL) restraints added in 1.9 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: 0.92 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: 3.68 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: 99.19 - 106.15: 186 106.15 - 113.10: 5466 113.10 - 120.06: 3222 120.06 - 127.01: 3954 127.01 - 133.97: 60 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: 5028 17.90 - 35.79: 480 35.79 - 53.69: 147 53.69 - 71.58: 21 71.58 - 89.48: 9 Dihedral angle restraints: 5685 sinusoidal: 2160 harmonic: 3525 Sorted by residual: dihedral pdb=" CB CYS B 269 " pdb=" SG CYS B 269 " pdb=" SG CYS B 441 " pdb=" CB CYS B 441 " ideal model delta sinusoidal sigma weight residual -86.00 -17.09 -68.91 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS C 269 " pdb=" SG CYS C 269 " pdb=" SG CYS C 441 " pdb=" CB CYS C 441 " ideal model delta sinusoidal sigma weight residual -86.00 -17.11 -68.89 1 1.00e+01 1.00e-02 6.14e+01 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 ... (remaining 5682 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: 9133 3.32 - 3.85: 15322 3.85 - 4.37: 17103 4.37 - 4.90: 31050 Nonbonded interactions: 74748 Sorted by model distance: nonbonded pdb=" O GLY B 392 " pdb=" OG1 THR B 396 " model vdw 2.264 2.440 nonbonded pdb=" O GLY A 392 " pdb=" OG1 THR A 396 " model vdw 2.265 2.440 nonbonded pdb=" O GLY C 392 " pdb=" OG1 THR C 396 " model vdw 2.265 2.440 nonbonded pdb=" O VAL C 20 " pdb=" OG1 THR C 24 " model vdw 2.316 2.440 nonbonded pdb=" O VAL B 20 " pdb=" OG1 THR B 24 " model vdw 2.316 2.440 ... (remaining 74743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.130 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: 5.990 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.410 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.060 ------------------------------------------------------------------------------- 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= 0.179 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 fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.048 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: 1.1462 time to fit residues: 168.2461 Evaluate side-chains 130 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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: 3.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8198 moved from start: 0.0699 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= 0.156 Angle : 0.497 7.716 12888 Z= 0.264 Chirality : 0.037 0.129 1635 Planarity : 0.004 0.032 1572 Dihedral : 3.584 13.774 1290 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.23 % Allowed : 20.53 % 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: 2.02 (0.24), residues: 1212 helix: 1.99 (0.16), residues: 972 sheet: 0.67 (0.64), residues: 54 loop : -2.07 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 19 HIS 0.001 0.000 HIS B 296 PHE 0.011 0.001 PHE C 240 TYR 0.008 0.001 TYR A 98 ARG 0.005 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 163 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 130 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7796 (tt0) cc_final: 0.7009 (tp-100) REVERT: A 437 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7802 (tt) REVERT: B 37 LEU cc_start: 0.7931 (tp) cc_final: 0.7618 (mp) REVERT: B 200 TYR cc_start: 0.7832 (m-80) cc_final: 0.7567 (m-80) REVERT: B 205 MET cc_start: 0.8720 (ptm) cc_final: 0.8496 (ptp) REVERT: B 248 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7006 (mpp) REVERT: B 252 GLN cc_start: 0.7823 (tt0) cc_final: 0.7018 (tp-100) REVERT: B 419 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6698 (ttt) REVERT: C 252 GLN cc_start: 0.7726 (tt0) cc_final: 0.6890 (tp-100) REVERT: C 473 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8493 (mtp) outliers start: 33 outliers final: 9 residues processed: 141 average time/residue: 1.2157 time to fit residues: 183.6352 Evaluate side-chains 141 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 67 ILE 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 248 MET Chi-restraints excluded: chain C residue 368 ASP 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: 4.9990 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.8200 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9495 Z= 0.155 Angle : 0.491 8.578 12888 Z= 0.260 Chirality : 0.037 0.127 1635 Planarity : 0.004 0.032 1572 Dihedral : 3.578 14.135 1290 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.13 % Allowed : 19.94 % 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: 2.04 (0.24), residues: 1212 helix: 2.01 (0.16), residues: 975 sheet: 0.35 (0.62), residues: 54 loop : -2.03 (0.38), 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 0.011 0.001 PHE C 240 TYR 0.007 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 164 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7803 (tt0) cc_final: 0.7007 (tp-100) REVERT: B 37 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7617 (mp) REVERT: B 200 TYR cc_start: 0.7855 (m-80) cc_final: 0.7556 (m-80) REVERT: B 205 MET cc_start: 0.8737 (ptm) cc_final: 0.8516 (ptp) REVERT: B 248 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7042 (mpp) REVERT: B 252 GLN cc_start: 0.7816 (tt0) cc_final: 0.7013 (tp-100) REVERT: B 329 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7043 (mpp) REVERT: B 419 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6733 (ttt) REVERT: C 252 GLN cc_start: 0.7732 (tt0) cc_final: 0.6887 (tp-100) REVERT: C 473 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8449 (mtp) outliers start: 32 outliers final: 13 residues processed: 142 average time/residue: 1.1194 time to fit residues: 170.8704 Evaluate side-chains 148 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 396 THR 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 368 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 248 MET Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 473 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 106 optimal weight: 0.0770 chunk 32 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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: 0.8180 moved from start: 0.0964 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= 0.143 Angle : 0.488 8.298 12888 Z= 0.253 Chirality : 0.036 0.175 1635 Planarity : 0.003 0.032 1572 Dihedral : 3.520 14.700 1290 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.64 % Allowed : 20.33 % 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: 2.10 (0.24), residues: 1212 helix: 2.06 (0.16), residues: 975 sheet: 0.18 (0.62), residues: 54 loop : -2.03 (0.39), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 19 HIS 0.001 0.000 HIS C 296 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 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 161 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7772 (tt0) cc_final: 0.6974 (tp-100) REVERT: A 312 ASN cc_start: 0.8315 (t0) cc_final: 0.8046 (t0) REVERT: B 37 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7590 (mp) REVERT: B 205 MET cc_start: 0.8716 (ptm) cc_final: 0.8482 (ptp) REVERT: B 248 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7027 (mpp) REVERT: B 252 GLN cc_start: 0.7785 (tt0) cc_final: 0.6992 (tp-100) REVERT: B 419 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6784 (ttt) REVERT: C 252 GLN cc_start: 0.7713 (tt0) cc_final: 0.6871 (tp-100) outliers start: 27 outliers final: 12 residues processed: 142 average time/residue: 1.1363 time to fit residues: 173.1910 Evaluate side-chains 146 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 368 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 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 368 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 30 optimal weight: 0.0370 chunk 40 optimal weight: 1.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- 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: 0.8189 moved from start: 0.1023 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= 0.151 Angle : 0.487 7.945 12888 Z= 0.255 Chirality : 0.037 0.175 1635 Planarity : 0.003 0.032 1572 Dihedral : 3.490 13.338 1290 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.83 % Allowed : 21.41 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.24), residues: 1212 helix: 2.07 (0.16), residues: 975 sheet: 0.09 (0.61), residues: 54 loop : -2.08 (0.39), 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 0.011 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 167 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7760 (tt0) cc_final: 0.6974 (tp-100) REVERT: A 437 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7861 (tt) REVERT: B 37 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7609 (mp) REVERT: B 200 TYR cc_start: 0.7813 (m-80) cc_final: 0.7533 (m-80) REVERT: B 205 MET cc_start: 0.8744 (ptm) cc_final: 0.8511 (ptp) REVERT: B 248 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7035 (mpp) REVERT: B 252 GLN cc_start: 0.7794 (tt0) cc_final: 0.6994 (tp-100) REVERT: B 322 GLN cc_start: 0.7660 (tt0) cc_final: 0.6793 (mt0) REVERT: B 329 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7057 (mpp) REVERT: B 406 ILE cc_start: 0.8510 (tt) cc_final: 0.8235 (tp) REVERT: B 419 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6721 (ttt) REVERT: C 252 GLN cc_start: 0.7723 (tt0) cc_final: 0.6882 (tp-100) outliers start: 29 outliers final: 15 residues processed: 146 average time/residue: 1.1306 time to fit residues: 177.3710 Evaluate side-chains 153 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 340 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 437 ILE 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 336 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 368 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 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 368 ASP 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: 0.8980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 0.0570 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1062 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 : 0.506 8.166 12888 Z= 0.267 Chirality : 0.038 0.182 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.550 13.514 1290 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.83 % Allowed : 21.51 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.24), residues: 1212 helix: 1.98 (0.16), residues: 975 sheet: 0.03 (0.60), residues: 54 loop : -2.13 (0.39), 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 0.002 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 fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 272 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7285 (mt-10) REVERT: A 322 GLN cc_start: 0.7708 (tt0) cc_final: 0.7018 (mt0) REVERT: A 396 THR cc_start: 0.8192 (p) cc_final: 0.7974 (t) REVERT: A 437 ILE cc_start: 0.8187 (tt) cc_final: 0.7962 (tt) REVERT: B 37 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7598 (mp) REVERT: B 200 TYR cc_start: 0.7833 (m-80) cc_final: 0.7498 (m-80) REVERT: B 205 MET cc_start: 0.8748 (ptm) cc_final: 0.8511 (ptp) REVERT: B 248 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7066 (mpp) REVERT: B 252 GLN cc_start: 0.7807 (tt0) cc_final: 0.6973 (tp-100) REVERT: B 318 MET cc_start: 0.7712 (mtm) cc_final: 0.7437 (ttm) REVERT: B 322 GLN cc_start: 0.7719 (tt0) cc_final: 0.6871 (mt0) REVERT: B 329 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7072 (mpp) REVERT: B 406 ILE cc_start: 0.8550 (tt) cc_final: 0.8279 (tp) REVERT: C 252 GLN cc_start: 0.7730 (tt0) cc_final: 0.6883 (tp-100) REVERT: C 322 GLN cc_start: 0.7717 (tt0) cc_final: 0.6841 (mp10) outliers start: 29 outliers final: 15 residues processed: 149 average time/residue: 1.0833 time to fit residues: 173.9866 Evaluate side-chains 152 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. 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 340 THR Chi-restraints excluded: chain A residue 351 ASP 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 336 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 368 ASP 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 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 368 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 100 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8194 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9495 Z= 0.155 Angle : 0.490 8.211 12888 Z= 0.259 Chirality : 0.037 0.184 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.513 13.380 1290 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.64 % Allowed : 21.70 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.24), residues: 1212 helix: 1.99 (0.16), residues: 975 sheet: 0.06 (0.61), residues: 54 loop : -2.12 (0.39), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 19 HIS 0.001 0.000 HIS C 296 PHE 0.011 0.001 PHE A 240 TYR 0.007 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 166 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7790 (tt0) cc_final: 0.7008 (tp-100) REVERT: A 272 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7250 (mt-10) REVERT: A 312 ASN cc_start: 0.8324 (t0) cc_final: 0.8040 (t0) REVERT: A 322 GLN cc_start: 0.7664 (tt0) cc_final: 0.6992 (mt0) REVERT: A 406 ILE cc_start: 0.8494 (tt) cc_final: 0.8283 (tp) REVERT: A 437 ILE cc_start: 0.8193 (tt) cc_final: 0.7972 (tt) REVERT: B 37 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7588 (mp) REVERT: B 200 TYR cc_start: 0.7860 (m-80) cc_final: 0.7542 (m-80) REVERT: B 205 MET cc_start: 0.8743 (ptm) cc_final: 0.8508 (ptp) REVERT: B 248 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7054 (mpp) REVERT: B 252 GLN cc_start: 0.7802 (tt0) cc_final: 0.7000 (tp-100) REVERT: B 318 MET cc_start: 0.7669 (mtm) cc_final: 0.7397 (ttm) REVERT: B 322 GLN cc_start: 0.7678 (tt0) cc_final: 0.6825 (mt0) REVERT: B 329 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7014 (mpp) REVERT: B 406 ILE cc_start: 0.8532 (tt) cc_final: 0.8270 (tp) REVERT: C 241 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8244 (m110) REVERT: C 252 GLN cc_start: 0.7719 (tt0) cc_final: 0.6880 (tp-100) REVERT: C 322 GLN cc_start: 0.7689 (tt0) cc_final: 0.6846 (mp10) outliers start: 27 outliers final: 16 residues processed: 150 average time/residue: 1.0849 time to fit residues: 174.9120 Evaluate side-chains 158 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 340 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 24 THR 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 336 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 368 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 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 368 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: 0.9990 chunk 35 optimal weight: 0.0570 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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: 0.8178 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9495 Z= 0.148 Angle : 0.482 8.103 12888 Z= 0.254 Chirality : 0.037 0.185 1635 Planarity : 0.004 0.032 1572 Dihedral : 3.471 13.310 1290 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.54 % Allowed : 21.99 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.24), residues: 1212 helix: 2.02 (0.16), residues: 975 sheet: 0.08 (0.61), residues: 54 loop : -2.08 (0.39), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 19 HIS 0.001 0.000 HIS C 296 PHE 0.009 0.001 PHE C 240 TYR 0.007 0.001 TYR C 98 ARG 0.007 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 167 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7778 (tt0) cc_final: 0.6994 (tp-100) REVERT: A 312 ASN cc_start: 0.8239 (t0) cc_final: 0.7963 (t0) REVERT: A 322 GLN cc_start: 0.7660 (tt0) cc_final: 0.6986 (mt0) REVERT: A 396 THR cc_start: 0.8269 (p) cc_final: 0.8030 (t) REVERT: A 406 ILE cc_start: 0.8515 (tt) cc_final: 0.8290 (tp) REVERT: A 437 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7931 (tt) REVERT: B 37 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7559 (mp) REVERT: B 200 TYR cc_start: 0.7881 (m-80) cc_final: 0.7577 (m-80) REVERT: B 205 MET cc_start: 0.8741 (ptm) cc_final: 0.8507 (ptp) REVERT: B 252 GLN cc_start: 0.7800 (tt0) cc_final: 0.6974 (tp-100) REVERT: B 318 MET cc_start: 0.7649 (mtm) cc_final: 0.7391 (ttm) REVERT: B 322 GLN cc_start: 0.7669 (tt0) cc_final: 0.6799 (mp10) REVERT: B 329 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6936 (mpp) REVERT: B 406 ILE cc_start: 0.8525 (tt) cc_final: 0.8265 (tp) REVERT: C 252 GLN cc_start: 0.7701 (tt0) cc_final: 0.6868 (tp-100) REVERT: C 322 GLN cc_start: 0.7668 (tt0) cc_final: 0.6829 (mp10) REVERT: C 406 ILE cc_start: 0.8506 (tt) cc_final: 0.8156 (tp) outliers start: 26 outliers final: 17 residues processed: 152 average time/residue: 1.0556 time to fit residues: 172.9412 Evaluate side-chains 157 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 340 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 368 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 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 368 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: 3.9990 chunk 113 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 116 optimal weight: 0.0060 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1166 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= 0.201 Angle : 0.538 8.534 12888 Z= 0.284 Chirality : 0.039 0.189 1635 Planarity : 0.004 0.035 1572 Dihedral : 3.615 13.680 1290 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.05 % Allowed : 22.29 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1212 helix: 1.86 (0.16), residues: 975 sheet: -0.09 (0.60), residues: 54 loop : -2.21 (0.38), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 256 HIS 0.001 0.000 HIS C 296 PHE 0.015 0.002 PHE A 240 TYR 0.009 0.001 TYR C 98 ARG 0.006 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 161 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 322 GLN cc_start: 0.7696 (tt0) cc_final: 0.6978 (mt0) REVERT: A 406 ILE cc_start: 0.8515 (tt) cc_final: 0.8295 (tp) REVERT: A 437 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7968 (tt) REVERT: B 37 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7727 (mt) REVERT: B 200 TYR cc_start: 0.7831 (m-80) cc_final: 0.7512 (m-80) REVERT: B 205 MET cc_start: 0.8767 (ptm) cc_final: 0.8530 (ptp) REVERT: B 252 GLN cc_start: 0.7871 (tt0) cc_final: 0.7037 (tp-100) REVERT: B 318 MET cc_start: 0.7746 (mtm) cc_final: 0.7484 (ttm) REVERT: B 322 GLN cc_start: 0.7730 (tt0) cc_final: 0.6830 (mp10) REVERT: B 406 ILE cc_start: 0.8565 (tt) cc_final: 0.8301 (tp) REVERT: B 419 MET cc_start: 0.6778 (ttt) cc_final: 0.6525 (ttt) REVERT: C 322 GLN cc_start: 0.7744 (tt0) cc_final: 0.6912 (mp10) REVERT: C 406 ILE cc_start: 0.8529 (tt) cc_final: 0.8173 (tp) REVERT: C 419 MET cc_start: 0.6675 (ttt) cc_final: 0.6320 (ttt) outliers start: 21 outliers final: 15 residues processed: 148 average time/residue: 1.1451 time to fit residues: 182.0621 Evaluate side-chains 155 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 368 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 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 368 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: 0.5980 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9495 Z= 0.211 Angle : 0.549 8.813 12888 Z= 0.290 Chirality : 0.039 0.199 1635 Planarity : 0.004 0.036 1572 Dihedral : 3.692 13.795 1290 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.05 % Allowed : 22.58 % Favored : 75.37 % 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: 1.64 (0.24), residues: 1212 helix: 1.77 (0.16), residues: 975 sheet: -0.16 (0.59), residues: 54 loop : -2.28 (0.38), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 256 HIS 0.002 0.001 HIS B 41 PHE 0.016 0.002 PHE A 240 TYR 0.009 0.001 TYR A 98 ARG 0.007 0.000 ARG B 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 158 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 322 GLN cc_start: 0.7721 (tt0) cc_final: 0.7000 (mt0) REVERT: A 437 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.8004 (tt) REVERT: B 200 TYR cc_start: 0.7830 (m-80) cc_final: 0.7504 (m-80) REVERT: B 205 MET cc_start: 0.8762 (ptm) cc_final: 0.8524 (ptp) REVERT: B 252 GLN cc_start: 0.7877 (tt0) cc_final: 0.7040 (tp-100) REVERT: B 318 MET cc_start: 0.7772 (mtm) cc_final: 0.7506 (ttm) REVERT: B 322 GLN cc_start: 0.7722 (tt0) cc_final: 0.6878 (mt0) REVERT: B 406 ILE cc_start: 0.8569 (tt) cc_final: 0.8297 (tp) REVERT: B 419 MET cc_start: 0.6758 (ttt) cc_final: 0.6489 (ttt) REVERT: C 322 GLN cc_start: 0.7789 (tt0) cc_final: 0.6950 (mp10) REVERT: C 419 MET cc_start: 0.6806 (ttt) cc_final: 0.6464 (ttt) outliers start: 21 outliers final: 15 residues processed: 148 average time/residue: 1.1035 time to fit residues: 175.5278 Evaluate side-chains 152 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 368 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 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 368 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: 0.7980 chunk 89 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.156824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111041 restraints weight = 9807.854| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.88 r_work: 0.3112 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9495 Z= 0.159 Angle : 0.508 8.721 12888 Z= 0.266 Chirality : 0.038 0.188 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.567 13.434 1290 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.96 % Allowed : 22.58 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.24), residues: 1212 helix: 2.08 (0.16), residues: 951 sheet: -0.03 (0.61), residues: 54 loop : -1.49 (0.39), residues: 207 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 0.010 0.001 PHE C 240 TYR 0.008 0.001 TYR C 98 ARG 0.007 0.000 ARG B 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3548.96 seconds wall clock time: 62 minutes 55.26 seconds (3775.26 seconds total)