Starting phenix.real_space_refine on Tue Jun 25 20:00:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvz_38724/06_2024/8xvz_38724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvz_38724/06_2024/8xvz_38724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvz_38724/06_2024/8xvz_38724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvz_38724/06_2024/8xvz_38724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvz_38724/06_2024/8xvz_38724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvz_38724/06_2024/8xvz_38724.pdb" } resolution = 3.78 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= 0.059 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 26 5.16 5 C 5745 2.51 5 N 1389 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B GLU 674": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8690 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4438 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 29, 'TRANS': 592} Chain breaks: 3 Unresolved non-hydrogen bonds: 600 Unresolved non-hydrogen angles: 750 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 4, 'ASP:plan': 4, 'PHE:plan': 10, 'GLU:plan': 19, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 359 Chain: "B" Number of atoms: 4252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4252 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'CIS': 1, 'PTRANS': 27, 'TRANS': 572} Chain breaks: 4 Unresolved non-hydrogen bonds: 618 Unresolved non-hydrogen angles: 773 Unresolved non-hydrogen dihedrals: 535 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 4, 'ASP:plan': 4, 'PHE:plan': 10, 'GLU:plan': 20, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 375 Time building chain proxies: 5.11, per 1000 atoms: 0.59 Number of scatterers: 8690 At special positions: 0 Unit cell: (75.96, 133.985, 98.115, 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 26 16.00 O 1530 8.00 N 1389 7.00 C 5745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 3.47 Conformation dependent library (CDL) restraints added in 1.5 seconds 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 68.6% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 3 through 26 removed outlier: 4.132A pdb=" N LEU A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 42 Processing helix chain 'A' and resid 56 through 67 removed outlier: 3.562A pdb=" N TRP A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 78 through 98 removed outlier: 3.791A pdb=" N ALA A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 151 through 185 removed outlier: 4.101A pdb=" N SER A 175 " --> pdb=" O TYR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 291 through 305 removed outlier: 3.516A pdb=" N GLU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 Processing helix chain 'A' and resid 355 through 378 removed outlier: 3.524A pdb=" N ARG A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.696A pdb=" N ARG A 395 " --> pdb=" O LYS A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 405 removed outlier: 5.269A pdb=" N LYS A 401 " --> pdb=" O PRO A 398 " (cutoff:3.500A) Proline residue: A 402 - end of helix Processing helix chain 'A' and resid 409 through 439 removed outlier: 3.898A pdb=" N LEU A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Proline residue: A 418 - end of helix Proline residue: A 430 - end of helix removed outlier: 3.569A pdb=" N LEU A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 465 Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 489 through 525 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.539A pdb=" N LYS A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 534 " --> pdb=" O PHE A 530 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS A 535 " --> pdb=" O HIS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 572 removed outlier: 3.530A pdb=" N GLY A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU A 566 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 578 No H-bonds generated for 'chain 'A' and resid 576 through 578' Processing helix chain 'A' and resid 579 through 596 Processing helix chain 'A' and resid 612 through 637 removed outlier: 3.515A pdb=" N ILE A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 662 Processing helix chain 'A' and resid 672 through 679 removed outlier: 3.656A pdb=" N GLU A 679 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 694 removed outlier: 3.854A pdb=" N ARG A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 694 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 27 removed outlier: 3.737A pdb=" N VAL B 8 " --> pdb=" O GLY B 4 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 33 removed outlier: 3.671A pdb=" N SER B 31 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 32 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 77 removed outlier: 3.967A pdb=" N VAL B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 98 removed outlier: 3.695A pdb=" N ALA B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.602A pdb=" N LEU B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 184 removed outlier: 3.566A pdb=" N PHE B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.530A pdb=" N LEU B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 303 Processing helix chain 'B' and resid 317 through 326 removed outlier: 3.797A pdb=" N GLN B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 removed outlier: 3.717A pdb=" N LEU B 347 " --> pdb=" O PRO B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 379 removed outlier: 3.737A pdb=" N ILE B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 386 Processing helix chain 'B' and resid 411 through 428 Proline residue: B 418 - end of helix removed outlier: 3.743A pdb=" N MET B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 439 Processing helix chain 'B' and resid 444 through 477 removed outlier: 4.270A pdb=" N ARG B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 513 Proline residue: B 499 - end of helix removed outlier: 4.454A pdb=" N LEU B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 510 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 523 removed outlier: 3.578A pdb=" N SER B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 560 through 571 removed outlier: 4.316A pdb=" N ILE B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU B 566 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 601 removed outlier: 4.013A pdb=" N LEU B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 Processing helix chain 'B' and resid 642 through 664 Proline residue: B 648 - end of helix Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 685 through 692 removed outlier: 3.884A pdb=" N ILE B 689 " --> pdb=" O ASP B 685 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 194 removed outlier: 3.590A pdb=" N VAL A 313 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ALA A 310 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 194 through 196 removed outlier: 3.680A pdb=" N ARG B 226 " --> pdb=" O PHE B 314 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1698 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: 2.59 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1517 1.32 - 1.45: 2333 1.45 - 1.57: 5019 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 8909 Sorted by residual: bond pdb=" CB VAL A 313 " pdb=" CG2 VAL A 313 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.15e+00 bond pdb=" C ASN A 596 " pdb=" O ASN A 596 " ideal model delta sigma weight residual 1.234 1.202 0.033 1.38e-02 5.25e+03 5.64e+00 bond pdb=" CB VAL B 15 " pdb=" CG2 VAL B 15 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.64e+00 bond pdb=" CB GLU A 619 " pdb=" CG GLU A 619 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.63e+00 bond pdb=" CB TRP A 336 " pdb=" CG TRP A 336 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.49e+00 ... (remaining 8904 not shown) Histogram of bond angle deviations from ideal: 95.33 - 103.09: 77 103.09 - 110.85: 3415 110.85 - 118.62: 3676 118.62 - 126.38: 4931 126.38 - 134.14: 140 Bond angle restraints: 12239 Sorted by residual: angle pdb=" N ASN B 237 " pdb=" CA ASN B 237 " pdb=" C ASN B 237 " ideal model delta sigma weight residual 113.18 102.45 10.73 1.33e+00 5.65e-01 6.50e+01 angle pdb=" CA ASN B 237 " pdb=" C ASN B 237 " pdb=" N LYS B 238 " ideal model delta sigma weight residual 118.22 113.55 4.67 1.03e+00 9.43e-01 2.06e+01 angle pdb=" N ILE A 525 " pdb=" CA ILE A 525 " pdb=" C ILE A 525 " ideal model delta sigma weight residual 112.35 117.58 -5.23 1.20e+00 6.94e-01 1.90e+01 angle pdb=" CG1 ILE A 379 " pdb=" CB ILE A 379 " pdb=" CG2 ILE A 379 " ideal model delta sigma weight residual 110.70 97.81 12.89 3.00e+00 1.11e-01 1.85e+01 angle pdb=" C MET A 378 " pdb=" N ILE A 379 " pdb=" CA ILE A 379 " ideal model delta sigma weight residual 122.13 129.60 -7.47 1.85e+00 2.92e-01 1.63e+01 ... (remaining 12234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4750 17.96 - 35.91: 323 35.91 - 53.87: 57 53.87 - 71.83: 5 71.83 - 89.78: 7 Dihedral angle restraints: 5142 sinusoidal: 1547 harmonic: 3595 Sorted by residual: dihedral pdb=" CA LYS B 235 " pdb=" C LYS B 235 " pdb=" N VAL B 236 " pdb=" CA VAL B 236 " ideal model delta harmonic sigma weight residual -180.00 -106.14 -73.86 0 5.00e+00 4.00e-02 2.18e+02 dihedral pdb=" CA VAL B 236 " pdb=" C VAL B 236 " pdb=" N ASN B 237 " pdb=" CA ASN B 237 " ideal model delta harmonic sigma weight residual 180.00 126.39 53.61 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA PHE B 513 " pdb=" C PHE B 513 " pdb=" N PHE B 514 " pdb=" CA PHE B 514 " ideal model delta harmonic sigma weight residual -180.00 -130.36 -49.64 0 5.00e+00 4.00e-02 9.85e+01 ... (remaining 5139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1127 0.059 - 0.117: 338 0.117 - 0.176: 42 0.176 - 0.234: 6 0.234 - 0.293: 3 Chirality restraints: 1516 Sorted by residual: chirality pdb=" CG LEU B 22 " pdb=" CB LEU B 22 " pdb=" CD1 LEU B 22 " pdb=" CD2 LEU B 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE A 379 " pdb=" CA ILE A 379 " pdb=" CG1 ILE A 379 " pdb=" CG2 ILE A 379 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB VAL A 313 " pdb=" CA VAL A 313 " pdb=" CG1 VAL A 313 " pdb=" CG2 VAL A 313 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1513 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 336 " -0.024 2.00e-02 2.50e+03 5.05e-02 6.37e+01 pdb=" CG TRP A 336 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 TRP A 336 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TRP A 336 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP A 336 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP A 336 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 336 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 336 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 336 " -0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP A 336 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 525 " -0.075 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO A 526 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 526 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 526 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 171 " 0.036 2.00e-02 2.50e+03 2.95e-02 1.74e+01 pdb=" CG TYR A 171 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR A 171 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 171 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 171 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 171 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR A 171 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 171 " -0.000 2.00e-02 2.50e+03 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 87 2.56 - 3.14: 8262 3.14 - 3.73: 13565 3.73 - 4.31: 17219 4.31 - 4.90: 28035 Nonbonded interactions: 67168 Sorted by model distance: nonbonded pdb=" O VAL A 593 " pdb=" O ASN A 596 " model vdw 1.969 3.040 nonbonded pdb=" OH TYR A 157 " pdb=" O LEU A 645 " model vdw 2.118 2.440 nonbonded pdb=" OE2 GLU B 343 " pdb=" OG SER B 446 " model vdw 2.141 2.440 nonbonded pdb=" OH TYR B 157 " pdb=" O LEU B 645 " model vdw 2.147 2.440 nonbonded pdb=" OG1 THR A 207 " pdb=" OE1 GLU A 210 " model vdw 2.170 2.440 ... (remaining 67163 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' and (resid 3 through 388 or (resid 410 and (name N or name CA or name \ C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N or \ name CA or name C or name O or name CB )) or resid 415 through 664 or (resid 66 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 666 through \ 696)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.030 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: 3.040 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.980 Find NCS groups from input model: 0.560 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.011 0.082 8909 Z= 0.699 Angle : 1.046 12.887 12239 Z= 0.576 Chirality : 0.054 0.293 1516 Planarity : 0.008 0.112 1520 Dihedral : 13.535 89.783 2804 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.33 % Allowed : 16.18 % Favored : 83.49 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 5.36 % Twisted General : 0.60 % 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: 1205 helix: -0.02 (0.19), residues: 762 sheet: -2.57 (1.12), residues: 26 loop : -4.02 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.116 0.005 TRP A 336 HIS 0.007 0.002 HIS A 617 PHE 0.041 0.003 PHE A 640 TYR 0.072 0.003 TYR A 171 ARG 0.007 0.001 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.961 Fit side-chains REVERT: A 465 PHE cc_start: 0.7191 (t80) cc_final: 0.6981 (t80) REVERT: B 618 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8109 (tm-30) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1650 time to fit residues: 40.4301 Evaluate side-chains 142 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 351 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8909 Z= 0.255 Angle : 0.797 13.328 12239 Z= 0.417 Chirality : 0.044 0.237 1516 Planarity : 0.007 0.099 1520 Dihedral : 7.221 74.089 1271 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.11 % Favored : 85.64 % Rotamer: Outliers : 2.17 % Allowed : 12.10 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 5.36 % Twisted General : 0.43 % 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: -1.46 (0.25), residues: 1205 helix: 0.42 (0.19), residues: 791 sheet: -1.76 (1.29), residues: 20 loop : -3.96 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 336 HIS 0.004 0.001 HIS B 617 PHE 0.038 0.002 PHE B 513 TYR 0.037 0.002 TYR A 171 ARG 0.002 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 1.135 Fit side-chains REVERT: A 190 GLU cc_start: 0.8521 (pp20) cc_final: 0.8050 (pp20) REVERT: A 215 TYR cc_start: 0.8383 (t80) cc_final: 0.7915 (t80) REVERT: A 369 PHE cc_start: 0.8960 (t80) cc_final: 0.8682 (t80) REVERT: A 374 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8134 (mp) REVERT: A 437 SER cc_start: 0.9187 (m) cc_final: 0.8631 (p) REVERT: B 199 MET cc_start: 0.8678 (tpp) cc_final: 0.8303 (mmm) REVERT: B 210 GLU cc_start: 0.8551 (pm20) cc_final: 0.8130 (pm20) REVERT: B 618 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7879 (tm-30) outliers start: 17 outliers final: 7 residues processed: 170 average time/residue: 0.1545 time to fit residues: 39.1868 Evaluate side-chains 151 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.0370 chunk 92 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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: 0.7844 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8909 Z= 0.237 Angle : 0.745 12.406 12239 Z= 0.387 Chirality : 0.042 0.185 1516 Planarity : 0.006 0.103 1520 Dihedral : 6.776 72.911 1271 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.53 % Favored : 86.22 % Rotamer: Outliers : 3.18 % Allowed : 17.32 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.52 % 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: -1.18 (0.25), residues: 1205 helix: 0.57 (0.19), residues: 793 sheet: 0.22 (1.84), residues: 10 loop : -3.72 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 336 HIS 0.005 0.001 HIS B 615 PHE 0.043 0.002 PHE B 513 TYR 0.028 0.001 TYR A 171 ARG 0.005 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8440 (pp20) cc_final: 0.8161 (pp20) REVERT: A 369 PHE cc_start: 0.9026 (t80) cc_final: 0.8638 (t80) REVERT: A 425 PHE cc_start: 0.7901 (t80) cc_final: 0.7556 (t80) REVERT: A 437 SER cc_start: 0.9126 (m) cc_final: 0.8576 (p) REVERT: A 620 ILE cc_start: 0.8301 (tt) cc_final: 0.7978 (tp) REVERT: B 72 ASP cc_start: 0.8250 (t0) cc_final: 0.8004 (t0) REVERT: B 199 MET cc_start: 0.8697 (tpp) cc_final: 0.8336 (mmm) REVERT: B 369 PHE cc_start: 0.8311 (t80) cc_final: 0.8099 (t80) REVERT: B 563 MET cc_start: 0.8325 (ttp) cc_final: 0.8055 (ttp) REVERT: B 618 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8018 (tm-30) REVERT: B 649 LEU cc_start: 0.8843 (mt) cc_final: 0.8603 (mt) outliers start: 25 outliers final: 11 residues processed: 178 average time/residue: 0.1563 time to fit residues: 41.5382 Evaluate side-chains 157 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 572 TYR Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7837 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8909 Z= 0.233 Angle : 0.743 12.025 12239 Z= 0.379 Chirality : 0.043 0.212 1516 Planarity : 0.006 0.104 1520 Dihedral : 6.575 72.456 1271 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.11 % Favored : 86.64 % Rotamer: Outliers : 2.68 % Allowed : 21.78 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % 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: -1.07 (0.25), residues: 1205 helix: 0.60 (0.19), residues: 794 sheet: 0.10 (1.80), residues: 10 loop : -3.55 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 336 HIS 0.004 0.001 HIS B 615 PHE 0.040 0.002 PHE B 513 TYR 0.023 0.002 TYR A 171 ARG 0.004 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 0.867 Fit side-chains REVERT: A 369 PHE cc_start: 0.9075 (t80) cc_final: 0.8619 (t80) REVERT: A 425 PHE cc_start: 0.7851 (t80) cc_final: 0.7569 (t80) REVERT: A 437 SER cc_start: 0.9081 (m) cc_final: 0.8538 (p) REVERT: B 72 ASP cc_start: 0.8216 (t0) cc_final: 0.7946 (t0) REVERT: B 199 MET cc_start: 0.8682 (tpp) cc_final: 0.8280 (mmm) REVERT: B 618 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7947 (tm-30) REVERT: B 631 MET cc_start: 0.9128 (mmp) cc_final: 0.8842 (mmp) REVERT: B 661 ARG cc_start: 0.7572 (tpt170) cc_final: 0.7308 (tpt170) outliers start: 21 outliers final: 10 residues processed: 174 average time/residue: 0.1493 time to fit residues: 39.1351 Evaluate side-chains 157 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8909 Z= 0.226 Angle : 0.742 13.544 12239 Z= 0.380 Chirality : 0.042 0.198 1516 Planarity : 0.006 0.103 1520 Dihedral : 6.420 71.856 1271 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.28 % Favored : 86.56 % Rotamer: Outliers : 3.06 % Allowed : 22.68 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % 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: -0.92 (0.25), residues: 1205 helix: 0.72 (0.19), residues: 794 sheet: 0.10 (1.86), residues: 10 loop : -3.51 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 336 HIS 0.005 0.001 HIS B 615 PHE 0.045 0.002 PHE B 513 TYR 0.020 0.001 TYR A 171 ARG 0.002 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8359 (mmt) cc_final: 0.8043 (mmt) REVERT: A 369 PHE cc_start: 0.9039 (t80) cc_final: 0.8543 (t80) REVERT: A 425 PHE cc_start: 0.7796 (t80) cc_final: 0.7569 (t80) REVERT: A 437 SER cc_start: 0.9049 (m) cc_final: 0.8523 (p) REVERT: A 620 ILE cc_start: 0.8261 (tt) cc_final: 0.7832 (tp) REVERT: B 72 ASP cc_start: 0.8225 (t0) cc_final: 0.7945 (t0) REVERT: B 199 MET cc_start: 0.8644 (tpp) cc_final: 0.8302 (mmm) REVERT: B 594 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9292 (mp) REVERT: B 618 GLN cc_start: 0.8366 (tm-30) cc_final: 0.8013 (tm-30) outliers start: 24 outliers final: 17 residues processed: 169 average time/residue: 0.1557 time to fit residues: 39.9742 Evaluate side-chains 166 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.0770 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.0870 chunk 118 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 0.0470 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 113 optimal weight: 0.0870 overall best weight: 0.1192 ------------------------------------------------------------------------------- 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: 0.7731 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8909 Z= 0.194 Angle : 0.723 13.833 12239 Z= 0.364 Chirality : 0.042 0.225 1516 Planarity : 0.006 0.104 1520 Dihedral : 6.190 70.172 1271 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.45 % Favored : 87.30 % Rotamer: Outliers : 3.44 % Allowed : 23.31 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % 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: -0.76 (0.25), residues: 1205 helix: 0.87 (0.19), residues: 790 sheet: 0.23 (1.88), residues: 10 loop : -3.47 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 336 HIS 0.003 0.001 HIS B 615 PHE 0.042 0.001 PHE B 513 TYR 0.033 0.001 TYR A 215 ARG 0.004 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8411 (mmt) cc_final: 0.8147 (mmt) REVERT: A 369 PHE cc_start: 0.9001 (t80) cc_final: 0.8551 (t80) REVERT: A 425 PHE cc_start: 0.7575 (t80) cc_final: 0.7367 (t80) REVERT: A 436 LEU cc_start: 0.8900 (mp) cc_final: 0.8483 (mt) REVERT: A 437 SER cc_start: 0.8977 (m) cc_final: 0.8436 (p) REVERT: A 466 ILE cc_start: 0.5819 (tp) cc_final: 0.5515 (mm) REVERT: A 620 ILE cc_start: 0.8080 (tt) cc_final: 0.7738 (tp) REVERT: B 72 ASP cc_start: 0.8103 (t0) cc_final: 0.7822 (t0) REVERT: B 231 THR cc_start: 0.7362 (OUTLIER) cc_final: 0.7033 (p) REVERT: B 618 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7982 (tm-30) outliers start: 27 outliers final: 17 residues processed: 183 average time/residue: 0.1483 time to fit residues: 40.9036 Evaluate side-chains 172 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8909 Z= 0.250 Angle : 0.760 16.321 12239 Z= 0.379 Chirality : 0.043 0.218 1516 Planarity : 0.006 0.105 1520 Dihedral : 6.142 69.439 1271 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.78 % Favored : 86.97 % Rotamer: Outliers : 3.44 % Allowed : 24.46 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % 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: -0.68 (0.26), residues: 1205 helix: 0.95 (0.19), residues: 791 sheet: 0.26 (1.90), residues: 10 loop : -3.48 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 336 HIS 0.003 0.001 HIS B 615 PHE 0.044 0.001 PHE B 513 TYR 0.021 0.001 TYR B 364 ARG 0.002 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7821 (mm-40) REVERT: A 437 SER cc_start: 0.9046 (m) cc_final: 0.8508 (p) REVERT: A 620 ILE cc_start: 0.8227 (tt) cc_final: 0.7843 (tp) REVERT: B 72 ASP cc_start: 0.8122 (t0) cc_final: 0.7848 (t0) REVERT: B 618 GLN cc_start: 0.8343 (tm-30) cc_final: 0.8072 (tm-30) outliers start: 27 outliers final: 22 residues processed: 175 average time/residue: 0.1499 time to fit residues: 39.8096 Evaluate side-chains 173 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.0370 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8909 Z= 0.206 Angle : 0.743 16.373 12239 Z= 0.369 Chirality : 0.042 0.209 1516 Planarity : 0.006 0.105 1520 Dihedral : 6.111 68.479 1271 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.70 % Favored : 87.05 % Rotamer: Outliers : 2.93 % Allowed : 24.71 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % 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: -0.61 (0.25), residues: 1205 helix: 1.03 (0.19), residues: 784 sheet: 0.24 (1.92), residues: 10 loop : -3.45 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 336 HIS 0.004 0.001 HIS B 615 PHE 0.042 0.001 PHE B 513 TYR 0.041 0.001 TYR A 215 ARG 0.006 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 369 PHE cc_start: 0.8941 (t80) cc_final: 0.8463 (t80) REVERT: A 436 LEU cc_start: 0.8938 (mp) cc_final: 0.8484 (mt) REVERT: A 437 SER cc_start: 0.8992 (m) cc_final: 0.8441 (p) REVERT: A 620 ILE cc_start: 0.8261 (tt) cc_final: 0.7784 (tp) REVERT: B 72 ASP cc_start: 0.8092 (t0) cc_final: 0.7833 (t0) REVERT: B 570 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7011 (t80) REVERT: B 618 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7943 (tm-30) outliers start: 23 outliers final: 20 residues processed: 171 average time/residue: 0.1506 time to fit residues: 38.5190 Evaluate side-chains 173 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.4980 chunk 102 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 0.0870 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8909 Z= 0.215 Angle : 0.752 15.255 12239 Z= 0.374 Chirality : 0.042 0.236 1516 Planarity : 0.006 0.105 1520 Dihedral : 6.025 67.281 1271 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.61 % Favored : 87.14 % Rotamer: Outliers : 3.31 % Allowed : 24.84 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % 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: -0.53 (0.25), residues: 1205 helix: 1.10 (0.19), residues: 784 sheet: 0.27 (1.92), residues: 10 loop : -3.44 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP A 336 HIS 0.004 0.001 HIS B 615 PHE 0.041 0.001 PHE B 513 TYR 0.020 0.001 TYR A 215 ARG 0.007 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 369 PHE cc_start: 0.8940 (t80) cc_final: 0.8419 (t80) REVERT: A 436 LEU cc_start: 0.8987 (mp) cc_final: 0.8547 (mt) REVERT: A 437 SER cc_start: 0.9016 (m) cc_final: 0.8459 (p) REVERT: A 620 ILE cc_start: 0.8134 (tt) cc_final: 0.7725 (tp) REVERT: B 72 ASP cc_start: 0.8041 (t0) cc_final: 0.7783 (t0) REVERT: B 231 THR cc_start: 0.7022 (OUTLIER) cc_final: 0.6764 (p) REVERT: B 570 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7116 (t80) REVERT: B 618 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7974 (tm-30) REVERT: B 661 ARG cc_start: 0.7409 (tpt170) cc_final: 0.6953 (tpt170) outliers start: 26 outliers final: 21 residues processed: 170 average time/residue: 0.1556 time to fit residues: 39.6708 Evaluate side-chains 176 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8909 Z= 0.219 Angle : 0.751 14.443 12239 Z= 0.373 Chirality : 0.042 0.227 1516 Planarity : 0.006 0.105 1520 Dihedral : 6.022 65.903 1271 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.53 % Favored : 87.22 % Rotamer: Outliers : 3.06 % Allowed : 25.99 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % 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: -0.51 (0.25), residues: 1205 helix: 1.17 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -3.40 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 336 HIS 0.003 0.001 HIS B 615 PHE 0.041 0.001 PHE B 513 TYR 0.020 0.001 TYR A 215 ARG 0.005 0.000 ARG B 661 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 351 ASN cc_start: 0.8884 (t0) cc_final: 0.8657 (t0) REVERT: A 369 PHE cc_start: 0.8890 (t80) cc_final: 0.8381 (t80) REVERT: A 436 LEU cc_start: 0.8952 (mp) cc_final: 0.8492 (mt) REVERT: A 437 SER cc_start: 0.8996 (m) cc_final: 0.8461 (p) REVERT: A 620 ILE cc_start: 0.8209 (tt) cc_final: 0.7722 (tp) REVERT: B 72 ASP cc_start: 0.8039 (t0) cc_final: 0.7785 (t0) REVERT: B 105 THR cc_start: 0.8417 (m) cc_final: 0.8197 (m) REVERT: B 231 THR cc_start: 0.6813 (OUTLIER) cc_final: 0.6606 (p) REVERT: B 376 PHE cc_start: 0.8193 (t80) cc_final: 0.7912 (t80) REVERT: B 381 ILE cc_start: 0.7880 (mm) cc_final: 0.7598 (mm) REVERT: B 570 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7175 (t80) REVERT: B 618 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 661 ARG cc_start: 0.7383 (tpt170) cc_final: 0.6948 (tpt170) outliers start: 24 outliers final: 20 residues processed: 176 average time/residue: 0.1526 time to fit residues: 40.0883 Evaluate side-chains 177 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 0.0570 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 85 optimal weight: 0.2980 chunk 5 optimal weight: 0.2980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.153067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117732 restraints weight = 15390.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.120427 restraints weight = 9374.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122223 restraints weight = 6876.493| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8909 Z= 0.206 Angle : 0.743 14.188 12239 Z= 0.368 Chirality : 0.042 0.227 1516 Planarity : 0.006 0.105 1520 Dihedral : 5.921 65.078 1271 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.45 % Favored : 87.30 % Rotamer: Outliers : 2.80 % Allowed : 25.73 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % 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: -0.41 (0.26), residues: 1205 helix: 1.25 (0.19), residues: 779 sheet: -1.90 (1.16), residues: 22 loop : -3.41 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 336 HIS 0.003 0.000 HIS B 615 PHE 0.040 0.001 PHE B 513 TYR 0.018 0.001 TYR A 377 ARG 0.006 0.000 ARG B 661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1691.29 seconds wall clock time: 30 minutes 58.84 seconds (1858.84 seconds total)