Starting phenix.real_space_refine on Sun Nov 17 11:02:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4k_41034/11_2024/8t4k_41034.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4k_41034/11_2024/8t4k_41034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4k_41034/11_2024/8t4k_41034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4k_41034/11_2024/8t4k_41034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4k_41034/11_2024/8t4k_41034.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4k_41034/11_2024/8t4k_41034.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.107 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 105 5.16 5 C 8562 2.51 5 N 2310 2.21 5 O 2583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13560 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3396 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 21, 'TRANS': 406} Chain breaks: 5 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 942 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Restraints were copied for chains: I, H, E, F, C, D Time building chain proxies: 12.50, per 1000 atoms: 0.92 Number of scatterers: 13560 At special positions: 0 Unit cell: (121.027, 123.431, 116.218, 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 105 16.00 O 2583 8.00 N 2310 7.00 C 8562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 156 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 295 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 386 " " NAG A 611 " - " ASN A 448 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 156 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 276 " " NAG C 607 " - " ASN C 295 " " NAG C 608 " - " ASN C 301 " " NAG C 609 " - " ASN C 332 " " NAG C 610 " - " ASN C 386 " " NAG C 611 " - " ASN C 448 " " NAG D 601 " - " ASN D 88 " " NAG D 602 " - " ASN D 156 " " NAG D 603 " - " ASN D 160 " " NAG D 604 " - " ASN D 197 " " NAG D 605 " - " ASN D 234 " " NAG D 606 " - " ASN D 276 " " NAG D 607 " - " ASN D 295 " " NAG D 608 " - " ASN D 301 " " NAG D 609 " - " ASN D 332 " " NAG D 610 " - " ASN D 386 " " NAG D 611 " - " ASN D 448 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN C 262 " " NAG I 1 " - " ASN D 262 " Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 2.1 seconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 21 sheets defined 28.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.048A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.906A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.437A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.570A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.311A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.529A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.048A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.906A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.437A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.570A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.311A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 removed outlier: 3.530A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 596 Processing helix chain 'E' and resid 618 through 625 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 662 Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.049A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 354 removed outlier: 3.906A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.437A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 removed outlier: 3.570A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.311A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.529A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.209A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.567A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.092A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.890A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.209A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.567A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.092A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.890A pdb=" N ASN C 301 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323A current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AB6, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.209A pdb=" N VAL D 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.566A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 75 through 76 Processing sheet with id=AB9, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AC2, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.092A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 259 through 261 current: chain 'D' and resid 284 through 312 removed outlier: 6.890A pdb=" N ASN D 301 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 315 through 323A current: chain 'D' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 381 through 385 current: chain 'D' and resid 465 through 470 459 hydrogen bonds defined for protein. 1251 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: 4.52 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4293 1.35 - 1.47: 3440 1.47 - 1.60: 5959 1.60 - 1.72: 0 1.72 - 1.85: 144 Bond restraints: 13836 Sorted by residual: bond pdb=" N GLU C 269 " pdb=" CA GLU C 269 " ideal model delta sigma weight residual 1.455 1.495 -0.041 1.29e-02 6.01e+03 9.97e+00 bond pdb=" N VAL D 270 " pdb=" CA VAL D 270 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.30e-02 5.92e+03 9.96e+00 bond pdb=" N VAL C 270 " pdb=" CA VAL C 270 " ideal model delta sigma weight residual 1.456 1.496 -0.041 1.30e-02 5.92e+03 9.89e+00 bond pdb=" N VAL A 270 " pdb=" CA VAL A 270 " ideal model delta sigma weight residual 1.456 1.496 -0.041 1.30e-02 5.92e+03 9.77e+00 bond pdb=" N GLU A 269 " pdb=" CA GLU A 269 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.29e-02 6.01e+03 9.65e+00 ... (remaining 13831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 16825 1.71 - 3.43: 1625 3.43 - 5.14: 249 5.14 - 6.85: 48 6.85 - 8.56: 12 Bond angle restraints: 18759 Sorted by residual: angle pdb=" CA PRO A 240 " pdb=" N PRO A 240 " pdb=" CD PRO A 240 " ideal model delta sigma weight residual 112.00 104.41 7.59 1.40e+00 5.10e-01 2.94e+01 angle pdb=" CA PRO D 240 " pdb=" N PRO D 240 " pdb=" CD PRO D 240 " ideal model delta sigma weight residual 112.00 104.43 7.57 1.40e+00 5.10e-01 2.93e+01 angle pdb=" CA PRO C 240 " pdb=" N PRO C 240 " pdb=" CD PRO C 240 " ideal model delta sigma weight residual 112.00 104.45 7.55 1.40e+00 5.10e-01 2.91e+01 angle pdb=" N GLN D 246 " pdb=" CA GLN D 246 " pdb=" C GLN D 246 " ideal model delta sigma weight residual 113.88 107.48 6.40 1.23e+00 6.61e-01 2.71e+01 angle pdb=" N GLN A 246 " pdb=" CA GLN A 246 " pdb=" C GLN A 246 " ideal model delta sigma weight residual 113.88 107.50 6.38 1.23e+00 6.61e-01 2.69e+01 ... (remaining 18754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 8181 17.71 - 35.42: 385 35.42 - 53.13: 143 53.13 - 70.84: 42 70.84 - 88.56: 24 Dihedral angle restraints: 8775 sinusoidal: 4041 harmonic: 4734 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.19 50.19 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -125.74 39.74 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" C CYS A 247 " pdb=" N CYS A 247 " pdb=" CA CYS A 247 " pdb=" CB CYS A 247 " ideal model delta harmonic sigma weight residual -122.60 -114.25 -8.35 0 2.50e+00 1.60e-01 1.12e+01 ... (remaining 8772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1960 0.108 - 0.216: 254 0.216 - 0.323: 3 0.323 - 0.431: 0 0.431 - 0.539: 3 Chirality restraints: 2220 Sorted by residual: chirality pdb=" CB ILE F 595 " pdb=" CA ILE F 595 " pdb=" CG1 ILE F 595 " pdb=" CG2 ILE F 595 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" CB ILE E 595 " pdb=" CA ILE E 595 " pdb=" CG1 ILE E 595 " pdb=" CG2 ILE E 595 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.24e+00 chirality pdb=" CB ILE B 595 " pdb=" CA ILE B 595 " pdb=" CG1 ILE B 595 " pdb=" CG2 ILE B 595 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.20e+00 ... (remaining 2217 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR F 639 " 0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C THR F 639 " -0.074 2.00e-02 2.50e+03 pdb=" O THR F 639 " 0.028 2.00e-02 2.50e+03 pdb=" N GLN F 640 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 639 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C THR E 639 " 0.073 2.00e-02 2.50e+03 pdb=" O THR E 639 " -0.027 2.00e-02 2.50e+03 pdb=" N GLN E 640 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 639 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C THR B 639 " 0.073 2.00e-02 2.50e+03 pdb=" O THR B 639 " -0.027 2.00e-02 2.50e+03 pdb=" N GLN B 640 " -0.025 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 9 2.00 - 2.73: 802 2.73 - 3.45: 17665 3.45 - 4.18: 35084 4.18 - 4.90: 58772 Nonbonded interactions: 112332 Sorted by model distance: nonbonded pdb=" NZ LYS B 655 " pdb=" SD MET E 535 " model vdw 1.281 3.480 nonbonded pdb=" NZ LYS E 655 " pdb=" SD MET F 535 " model vdw 1.281 3.480 nonbonded pdb=" SD MET B 535 " pdb=" NZ LYS F 655 " model vdw 1.282 3.480 nonbonded pdb=" CE LYS B 655 " pdb=" SD MET E 535 " model vdw 1.447 3.800 nonbonded pdb=" SD MET B 535 " pdb=" CE LYS F 655 " model vdw 1.447 3.800 ... (remaining 112327 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 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 39.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 35.370 Find NCS groups from input model: 0.540 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: 0.010 Load rotamer database and sin/cos tables:14.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.007 0.084 13836 Z= 0.459 Angle : 1.097 8.565 18759 Z= 0.632 Chirality : 0.067 0.539 2220 Planarity : 0.008 0.078 2316 Dihedral : 13.194 88.556 5670 Min Nonbonded Distance : 1.281 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.94 % Favored : 98.87 % Rotamer: Outliers : 0.62 % Allowed : 7.22 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1590 helix: 0.19 (0.24), residues: 414 sheet: 0.72 (0.22), residues: 462 loop : 1.14 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP C 479 HIS 0.033 0.004 HIS C 66 PHE 0.022 0.003 PHE A 383 TYR 0.012 0.003 TYR E 643 ARG 0.014 0.002 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 213 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.9001 (mmp) cc_final: 0.8733 (mpp) REVERT: B 588 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.7665 (ttp-110) REVERT: C 325 HIS cc_start: 0.7525 (m90) cc_final: 0.7130 (m90) REVERT: C 419 TRP cc_start: 0.8225 (m-90) cc_final: 0.7796 (m100) REVERT: E 588 ARG cc_start: 0.7837 (ttp-110) cc_final: 0.7441 (ttp-110) REVERT: D 166 ARG cc_start: 0.8043 (ttp80) cc_final: 0.6570 (mmt90) REVERT: D 327 ARG cc_start: 0.7529 (mtm180) cc_final: 0.7224 (mmt180) REVERT: F 588 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7706 (ttp-110) outliers start: 9 outliers final: 0 residues processed: 219 average time/residue: 1.5228 time to fit residues: 361.1756 Evaluate side-chains 189 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 352 HIS E 591 GLN ** E 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 HIS ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13836 Z= 0.346 Angle : 0.654 11.091 18759 Z= 0.350 Chirality : 0.050 0.185 2220 Planarity : 0.005 0.045 2316 Dihedral : 5.379 22.653 2553 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.89 % Allowed : 8.04 % Favored : 89.07 % 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: 1.22 (0.20), residues: 1590 helix: 1.35 (0.27), residues: 417 sheet: 0.78 (0.22), residues: 456 loop : 0.69 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 479 HIS 0.007 0.001 HIS C 66 PHE 0.014 0.003 PHE C 53 TYR 0.014 0.002 TYR A 217 ARG 0.004 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 ARG cc_start: 0.7955 (mmt180) cc_final: 0.7498 (mmt90) REVERT: C 166 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8190 (ttp80) REVERT: C 347 LYS cc_start: 0.7503 (pttp) cc_final: 0.7168 (pptt) REVERT: C 500 ARG cc_start: 0.7840 (mmt180) cc_final: 0.7447 (mmt90) REVERT: E 588 ARG cc_start: 0.7890 (ttp-110) cc_final: 0.7474 (ttp-110) REVERT: D 500 ARG cc_start: 0.7731 (mmt180) cc_final: 0.7275 (mmt90) REVERT: F 601 LYS cc_start: 0.7252 (mptt) cc_final: 0.7039 (mmmm) REVERT: F 633 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6365 (mtpt) outliers start: 42 outliers final: 15 residues processed: 223 average time/residue: 1.4509 time to fit residues: 351.1178 Evaluate side-chains 203 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 352 HIS E 591 GLN E 640 GLN D 352 HIS ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13836 Z= 0.298 Angle : 0.596 12.742 18759 Z= 0.315 Chirality : 0.048 0.177 2220 Planarity : 0.004 0.037 2316 Dihedral : 5.373 23.751 2553 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.37 % Allowed : 9.42 % Favored : 87.22 % 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: 1.16 (0.21), residues: 1590 helix: 1.49 (0.27), residues: 420 sheet: 0.86 (0.22), residues: 456 loop : 0.41 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 479 HIS 0.004 0.001 HIS D 352 PHE 0.013 0.002 PHE A 383 TYR 0.012 0.002 TYR A 217 ARG 0.005 0.000 ARG E 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 179 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7037 (t) cc_final: 0.6690 (t) REVERT: A 328 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8455 (tpt) REVERT: A 500 ARG cc_start: 0.7813 (mmt180) cc_final: 0.7349 (mtt-85) REVERT: B 633 LYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6384 (mtpt) REVERT: B 661 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6885 (mp) REVERT: C 347 LYS cc_start: 0.7559 (pttp) cc_final: 0.7195 (pptt) REVERT: C 500 ARG cc_start: 0.7808 (mmt180) cc_final: 0.7403 (mmt90) REVERT: E 535 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7757 (mmm) REVERT: E 588 ARG cc_start: 0.7892 (ttp-110) cc_final: 0.7403 (ttp-110) REVERT: D 268 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6697 (pt0) REVERT: F 601 LYS cc_start: 0.7381 (mptt) cc_final: 0.7152 (mmmm) REVERT: F 633 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6373 (mtpt) outliers start: 49 outliers final: 18 residues processed: 209 average time/residue: 1.5071 time to fit residues: 341.2900 Evaluate side-chains 198 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** E 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN D 352 HIS ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13836 Z= 0.211 Angle : 0.536 14.156 18759 Z= 0.282 Chirality : 0.045 0.154 2220 Planarity : 0.004 0.038 2316 Dihedral : 5.069 24.264 2553 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.02 % Allowed : 10.86 % Favored : 86.12 % 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: 1.32 (0.21), residues: 1590 helix: 1.63 (0.27), residues: 420 sheet: 1.12 (0.23), residues: 432 loop : 0.41 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 479 HIS 0.003 0.001 HIS D 352 PHE 0.013 0.002 PHE D 53 TYR 0.011 0.001 TYR A 217 ARG 0.003 0.000 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.6941 (t) cc_final: 0.6622 (t) REVERT: A 151 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7954 (ttm170) REVERT: A 328 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8439 (tpt) REVERT: A 430 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7893 (mp) REVERT: A 500 ARG cc_start: 0.7808 (mmt180) cc_final: 0.7382 (mtt-85) REVERT: C 103 GLN cc_start: 0.8131 (mt0) cc_final: 0.7010 (tm-30) REVERT: C 137 LYS cc_start: 0.7655 (mttt) cc_final: 0.6796 (pmtt) REVERT: C 347 LYS cc_start: 0.7555 (pttp) cc_final: 0.7237 (pptt) REVERT: E 535 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7772 (mmm) outliers start: 44 outliers final: 16 residues processed: 201 average time/residue: 1.5517 time to fit residues: 337.5998 Evaluate side-chains 188 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 0.3980 chunk 2 optimal weight: 0.0970 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 0.0470 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN E 591 GLN D 352 HIS F 585 HIS F 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 13836 Z= 0.158 Angle : 0.505 13.613 18759 Z= 0.265 Chirality : 0.044 0.156 2220 Planarity : 0.003 0.031 2316 Dihedral : 4.743 24.191 2553 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.89 % Allowed : 11.75 % Favored : 85.36 % 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: 1.35 (0.21), residues: 1590 helix: 1.81 (0.27), residues: 420 sheet: 1.15 (0.24), residues: 420 loop : 0.32 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 479 HIS 0.003 0.001 HIS D 105 PHE 0.008 0.001 PHE D 53 TYR 0.013 0.001 TYR A 217 ARG 0.002 0.000 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.6863 (t) cc_final: 0.6567 (t) REVERT: A 151 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7925 (ttm170) REVERT: A 328 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8368 (tpt) REVERT: A 500 ARG cc_start: 0.7819 (mmt180) cc_final: 0.7379 (mmt90) REVERT: B 657 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6832 (tp30) REVERT: B 661 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6737 (mp) REVERT: C 103 GLN cc_start: 0.8096 (mt0) cc_final: 0.6995 (tm-30) REVERT: C 137 LYS cc_start: 0.7620 (mttt) cc_final: 0.6755 (pmtt) REVERT: C 325 HIS cc_start: 0.7539 (m-70) cc_final: 0.7186 (m170) REVERT: C 347 LYS cc_start: 0.7540 (pttp) cc_final: 0.7164 (pptt) REVERT: E 535 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7753 (mmm) REVERT: D 114 GLN cc_start: 0.7540 (mt0) cc_final: 0.7254 (pt0) outliers start: 42 outliers final: 14 residues processed: 198 average time/residue: 1.5903 time to fit residues: 342.8639 Evaluate side-chains 187 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN E 591 GLN F 591 GLN F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13836 Z= 0.314 Angle : 0.604 14.437 18759 Z= 0.313 Chirality : 0.048 0.181 2220 Planarity : 0.004 0.038 2316 Dihedral : 5.217 23.388 2553 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.89 % Allowed : 11.55 % Favored : 85.57 % 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: 1.15 (0.21), residues: 1590 helix: 1.57 (0.27), residues: 420 sheet: 1.03 (0.23), residues: 426 loop : 0.25 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 479 HIS 0.003 0.001 HIS A 249 PHE 0.013 0.002 PHE A 383 TYR 0.012 0.002 TYR A 217 ARG 0.004 0.001 ARG F 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.6955 (t) cc_final: 0.6654 (t) REVERT: A 114 GLN cc_start: 0.7609 (mt0) cc_final: 0.7386 (pt0) REVERT: A 500 ARG cc_start: 0.7802 (mmt180) cc_final: 0.7408 (mtt-85) REVERT: B 633 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6423 (mtpt) REVERT: B 634 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7420 (mt-10) REVERT: B 657 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6819 (tp30) REVERT: B 661 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6788 (mp) REVERT: C 83 GLU cc_start: 0.7804 (tt0) cc_final: 0.7573 (tm-30) REVERT: C 103 GLN cc_start: 0.8100 (mt0) cc_final: 0.6991 (tm-30) REVERT: C 137 LYS cc_start: 0.7673 (mttt) cc_final: 0.6792 (pmtt) REVERT: C 151 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.8107 (ttt180) REVERT: C 347 LYS cc_start: 0.7549 (pttp) cc_final: 0.7188 (pptt) REVERT: C 500 ARG cc_start: 0.7882 (mmt180) cc_final: 0.7397 (mtt-85) REVERT: E 535 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7760 (mmm) REVERT: D 47 ASP cc_start: 0.8006 (m-30) cc_final: 0.7737 (m-30) REVERT: D 166 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8179 (tmm160) REVERT: D 327 ARG cc_start: 0.7789 (mtm180) cc_final: 0.7445 (mmt180) REVERT: F 633 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6400 (mtpt) REVERT: F 657 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7049 (tp30) outliers start: 42 outliers final: 22 residues processed: 196 average time/residue: 1.5489 time to fit residues: 328.3225 Evaluate side-chains 192 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 0.0050 chunk 85 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 94 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN C 114 GLN E 591 GLN F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13836 Z= 0.174 Angle : 0.516 12.116 18759 Z= 0.270 Chirality : 0.044 0.155 2220 Planarity : 0.003 0.033 2316 Dihedral : 4.886 24.149 2553 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.68 % Allowed : 12.10 % Favored : 85.22 % 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: 1.25 (0.21), residues: 1590 helix: 1.77 (0.27), residues: 420 sheet: 1.03 (0.23), residues: 426 loop : 0.27 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 479 HIS 0.002 0.001 HIS D 105 PHE 0.012 0.001 PHE C 53 TYR 0.010 0.001 TYR A 217 ARG 0.003 0.000 ARG F 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.6864 (t) cc_final: 0.6595 (t) REVERT: A 137 LYS cc_start: 0.7578 (mttt) cc_final: 0.6786 (pmtt) REVERT: A 166 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7075 (ttp80) REVERT: A 328 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8377 (tpt) REVERT: A 430 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7867 (mp) REVERT: A 500 ARG cc_start: 0.7824 (mmt180) cc_final: 0.7386 (mtt-85) REVERT: B 633 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6452 (mtpt) REVERT: B 634 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7356 (mt-10) REVERT: C 103 GLN cc_start: 0.8058 (mt0) cc_final: 0.6979 (tm-30) REVERT: C 137 LYS cc_start: 0.7676 (mttt) cc_final: 0.6803 (pmtt) REVERT: C 151 ARG cc_start: 0.8278 (ttm-80) cc_final: 0.8075 (ttt180) REVERT: C 347 LYS cc_start: 0.7508 (pttp) cc_final: 0.7137 (pptt) REVERT: C 500 ARG cc_start: 0.7876 (mmt180) cc_final: 0.7392 (mtt-85) REVERT: E 535 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7771 (mmm) REVERT: D 114 GLN cc_start: 0.7552 (mt0) cc_final: 0.7349 (pt0) REVERT: D 141 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7379 (ttm) REVERT: D 166 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7276 (ttp80) REVERT: D 327 ARG cc_start: 0.7779 (mtm180) cc_final: 0.7408 (mmt180) REVERT: D 347 LYS cc_start: 0.7477 (pttp) cc_final: 0.7126 (pptt) outliers start: 39 outliers final: 17 residues processed: 189 average time/residue: 1.5604 time to fit residues: 318.9923 Evaluate side-chains 186 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 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 114 GLN B 591 GLN E 591 GLN F 591 GLN F 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13836 Z= 0.303 Angle : 0.594 13.241 18759 Z= 0.307 Chirality : 0.048 0.177 2220 Planarity : 0.004 0.038 2316 Dihedral : 5.189 23.545 2553 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.41 % Allowed : 12.51 % Favored : 85.09 % 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: 1.14 (0.21), residues: 1590 helix: 1.67 (0.26), residues: 417 sheet: 0.99 (0.23), residues: 426 loop : 0.19 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 69 HIS 0.003 0.001 HIS E 585 PHE 0.012 0.002 PHE A 383 TYR 0.011 0.002 TYR D 384 ARG 0.004 0.000 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.6966 (t) cc_final: 0.6697 (t) REVERT: A 166 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7073 (ttp80) REVERT: A 430 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7857 (mp) REVERT: A 500 ARG cc_start: 0.7816 (mmt180) cc_final: 0.7396 (mtt-85) REVERT: B 633 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6456 (mtpt) REVERT: C 103 GLN cc_start: 0.8098 (mt0) cc_final: 0.6999 (tm-30) REVERT: C 137 LYS cc_start: 0.7667 (mttt) cc_final: 0.6789 (pmtt) REVERT: C 151 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.8103 (ttt180) REVERT: C 347 LYS cc_start: 0.7532 (pttp) cc_final: 0.7163 (pptt) REVERT: C 500 ARG cc_start: 0.7858 (mmt180) cc_final: 0.7398 (mtt-85) REVERT: E 535 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7773 (mmm) REVERT: D 47 ASP cc_start: 0.8025 (m-30) cc_final: 0.7756 (m-30) REVERT: D 114 GLN cc_start: 0.7575 (mt0) cc_final: 0.7348 (pt0) REVERT: D 166 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8190 (tmm160) REVERT: D 327 ARG cc_start: 0.7756 (mtm180) cc_final: 0.7500 (mmt180) REVERT: D 347 LYS cc_start: 0.7515 (pttp) cc_final: 0.7148 (pptt) outliers start: 35 outliers final: 24 residues processed: 186 average time/residue: 1.5283 time to fit residues: 307.6649 Evaluate side-chains 193 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 591 GLN E 591 GLN F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13836 Z= 0.277 Angle : 0.589 13.012 18759 Z= 0.305 Chirality : 0.047 0.181 2220 Planarity : 0.004 0.036 2316 Dihedral : 5.251 23.906 2553 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.34 % Allowed : 12.99 % Favored : 84.67 % 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: 1.12 (0.21), residues: 1590 helix: 1.65 (0.26), residues: 417 sheet: 1.01 (0.23), residues: 420 loop : 0.16 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 479 HIS 0.002 0.001 HIS A 249 PHE 0.011 0.002 PHE A 383 TYR 0.011 0.002 TYR A 384 ARG 0.005 0.000 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.6999 (t) cc_final: 0.6729 (t) REVERT: A 166 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7087 (ttp80) REVERT: A 328 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8390 (tpt) REVERT: A 430 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7853 (mp) REVERT: A 500 ARG cc_start: 0.7821 (mmt180) cc_final: 0.7389 (mtt-85) REVERT: B 633 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6452 (mtpt) REVERT: C 137 LYS cc_start: 0.7683 (mttt) cc_final: 0.6811 (pmtt) REVERT: C 151 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.8062 (ttt180) REVERT: C 325 HIS cc_start: 0.7551 (m-70) cc_final: 0.7193 (m170) REVERT: C 347 LYS cc_start: 0.7527 (pttp) cc_final: 0.7160 (pptt) REVERT: C 500 ARG cc_start: 0.7873 (mmt180) cc_final: 0.7416 (mtt-85) REVERT: E 535 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7801 (mmm) REVERT: E 588 ARG cc_start: 0.7843 (ttp-110) cc_final: 0.7594 (ttp-110) REVERT: D 47 ASP cc_start: 0.8033 (m-30) cc_final: 0.7733 (m-30) REVERT: D 114 GLN cc_start: 0.7574 (mt0) cc_final: 0.7364 (pt0) REVERT: D 166 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8245 (tmm160) REVERT: D 327 ARG cc_start: 0.7727 (mtm180) cc_final: 0.7458 (mmt180) REVERT: D 347 LYS cc_start: 0.7525 (pttp) cc_final: 0.7155 (pptt) REVERT: F 588 ARG cc_start: 0.7838 (ttp-110) cc_final: 0.7398 (ttp80) outliers start: 34 outliers final: 23 residues processed: 185 average time/residue: 1.5369 time to fit residues: 307.3265 Evaluate side-chains 194 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 591 GLN E 591 GLN F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13836 Z= 0.235 Angle : 0.565 12.395 18759 Z= 0.293 Chirality : 0.046 0.176 2220 Planarity : 0.004 0.037 2316 Dihedral : 5.154 23.979 2553 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.34 % Allowed : 13.13 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1590 helix: 1.73 (0.27), residues: 417 sheet: 1.03 (0.23), residues: 420 loop : 0.17 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 419 HIS 0.002 0.001 HIS C 105 PHE 0.011 0.001 PHE D 53 TYR 0.010 0.001 TYR A 217 ARG 0.004 0.000 ARG B 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.6978 (t) cc_final: 0.6716 (t) REVERT: A 166 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7082 (ttp80) REVERT: A 328 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8380 (tpt) REVERT: A 430 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7917 (mp) REVERT: A 466 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7638 (mm-30) REVERT: A 500 ARG cc_start: 0.7836 (mmt180) cc_final: 0.7398 (mtt-85) REVERT: B 633 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6439 (mtpt) REVERT: C 137 LYS cc_start: 0.7684 (mttt) cc_final: 0.6811 (pmtt) REVERT: C 325 HIS cc_start: 0.7498 (m-70) cc_final: 0.7156 (m170) REVERT: C 347 LYS cc_start: 0.7523 (pttp) cc_final: 0.7155 (pptt) REVERT: C 500 ARG cc_start: 0.7857 (mmt180) cc_final: 0.7407 (mtt-85) REVERT: E 535 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7791 (mmm) REVERT: E 588 ARG cc_start: 0.7821 (ttp-110) cc_final: 0.7595 (ttp-110) REVERT: D 47 ASP cc_start: 0.7950 (m-30) cc_final: 0.7689 (m-30) REVERT: D 166 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8177 (tmm160) REVERT: D 327 ARG cc_start: 0.7757 (mtm180) cc_final: 0.7395 (mmt180) REVERT: D 347 LYS cc_start: 0.7519 (pttp) cc_final: 0.7156 (pptt) REVERT: F 588 ARG cc_start: 0.7823 (ttp-110) cc_final: 0.7486 (ttp-110) outliers start: 34 outliers final: 23 residues processed: 184 average time/residue: 1.5657 time to fit residues: 311.0054 Evaluate side-chains 193 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 591 GLN E 591 GLN D 114 GLN F 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.151720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125357 restraints weight = 14125.183| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.43 r_work: 0.3297 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13836 Z= 0.226 Angle : 0.559 12.017 18759 Z= 0.290 Chirality : 0.046 0.184 2220 Planarity : 0.004 0.036 2316 Dihedral : 5.092 23.798 2553 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.20 % Allowed : 13.40 % Favored : 84.40 % 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: 1.16 (0.21), residues: 1590 helix: 1.75 (0.27), residues: 417 sheet: 1.03 (0.23), residues: 420 loop : 0.15 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 419 HIS 0.002 0.001 HIS C 105 PHE 0.011 0.001 PHE C 53 TYR 0.010 0.001 TYR A 217 ARG 0.008 0.000 ARG B 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5762.05 seconds wall clock time: 106 minutes 20.57 seconds (6380.57 seconds total)