Starting phenix.real_space_refine on Wed Sep 25 13:28:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sun_25442/09_2024/7sun_25442.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sun_25442/09_2024/7sun_25442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sun_25442/09_2024/7sun_25442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sun_25442/09_2024/7sun_25442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sun_25442/09_2024/7sun_25442.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sun_25442/09_2024/7sun_25442.cif" } resolution = 3.6 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= 0.000 sd= 0.005 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 52 5.16 5 C 6852 2.51 5 N 1692 2.21 5 O 1858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10454 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5227 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 642} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Restraints were copied for chains: B Time building chain proxies: 9.62, per 1000 atoms: 0.92 Number of scatterers: 10454 At special positions: 0 Unit cell: (101.46, 116.412, 115.344, 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 52 16.00 O 1858 8.00 N 1692 7.00 C 6852 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.3 seconds 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2504 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 5 sheets defined 70.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 41 through 48 removed outlier: 3.640A pdb=" N LYS A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 71 removed outlier: 3.695A pdb=" N TRP A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 66 through 71' Processing helix chain 'A' and resid 75 through 105 removed outlier: 4.053A pdb=" N VAL A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLY A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 108 through 115 removed outlier: 3.840A pdb=" N GLY A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'A' and resid 168 through 196 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 206 through 230 removed outlier: 4.479A pdb=" N LYS A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 258 through 282 removed outlier: 3.962A pdb=" N LEU A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 308 removed outlier: 3.821A pdb=" N PHE A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.636A pdb=" N SER A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 removed outlier: 4.045A pdb=" N HIS A 337 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 366 Processing helix chain 'A' and resid 370 through 387 removed outlier: 3.896A pdb=" N LEU A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 407 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.786A pdb=" N GLU A 433 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 removed outlier: 3.672A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 455 removed outlier: 3.826A pdb=" N MET A 453 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 463 removed outlier: 3.630A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 463 " --> pdb=" O PRO A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 Processing helix chain 'A' and resid 483 through 505 removed outlier: 4.205A pdb=" N ILE A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 560 removed outlier: 4.819A pdb=" N ASP A 550 " --> pdb=" O TYR A 546 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 579 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 653 through 671 Processing helix chain 'A' and resid 680 through 690 removed outlier: 3.568A pdb=" N ASN A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 694 removed outlier: 3.545A pdb=" N GLU A 694 " --> pdb=" O ARG A 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 694' Processing helix chain 'A' and resid 695 through 700 removed outlier: 3.644A pdb=" N LYS A 699 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU A 700 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 726 Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 41 through 48 removed outlier: 3.639A pdb=" N LYS B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 71 removed outlier: 3.696A pdb=" N TRP B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 66 through 71' Processing helix chain 'B' and resid 75 through 105 removed outlier: 4.052A pdb=" N VAL B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLY B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 108 through 115 removed outlier: 3.841A pdb=" N GLY B 112 " --> pdb=" O PRO B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 Processing helix chain 'B' and resid 137 through 152 Processing helix chain 'B' and resid 168 through 196 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 206 through 230 removed outlier: 4.479A pdb=" N LYS B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 258 through 282 removed outlier: 3.962A pdb=" N LEU B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 308 removed outlier: 3.821A pdb=" N PHE B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.636A pdb=" N SER B 312 " --> pdb=" O ASN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 338 removed outlier: 4.045A pdb=" N HIS B 337 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 366 Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.897A pdb=" N LEU B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 407 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.786A pdb=" N GLU B 433 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 449 removed outlier: 3.673A pdb=" N LEU B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.825A pdb=" N MET B 453 " --> pdb=" O GLY B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 463 removed outlier: 3.631A pdb=" N PHE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 463 " --> pdb=" O PRO B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 481 Processing helix chain 'B' and resid 483 through 505 removed outlier: 4.204A pdb=" N ILE B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 560 removed outlier: 4.819A pdb=" N ASP B 550 " --> pdb=" O TYR B 546 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 579 Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 653 through 671 Processing helix chain 'B' and resid 680 through 690 removed outlier: 3.569A pdb=" N ASN B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 694 removed outlier: 3.545A pdb=" N GLU B 694 " --> pdb=" O ARG B 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 691 through 694' Processing helix chain 'B' and resid 695 through 700 removed outlier: 3.643A pdb=" N LYS B 699 " --> pdb=" O PRO B 696 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU B 700 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 726 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.870A pdb=" N VAL A 18 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 18 " --> pdb=" O VAL A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 135 removed outlier: 4.684A pdb=" N SER A 133 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.190A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N GLN A 513 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 11.379A pdb=" N ILE A 535 " --> pdb=" O GLN A 513 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LYS A 536 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP A 645 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE A 538 " --> pdb=" O ASP A 645 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 677 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE A 703 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 676 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.684A pdb=" N SER B 133 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.190A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N GLN B 513 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 11.379A pdb=" N ILE B 535 " --> pdb=" O GLN B 513 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS B 536 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP B 645 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE B 538 " --> pdb=" O ASP B 645 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 677 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE B 703 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 676 " --> pdb=" O PHE B 703 " (cutoff:3.500A) 658 hydrogen bonds defined for protein. 1896 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: 3.41 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3240 1.34 - 1.46: 2332 1.46 - 1.58: 5028 1.58 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 10686 Sorted by residual: bond pdb=" CG LEU B 401 " pdb=" CD1 LEU B 401 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.41e+00 bond pdb=" CG LEU A 401 " pdb=" CD1 LEU A 401 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.38e+00 bond pdb=" CA GLU B 527 " pdb=" C GLU B 527 " ideal model delta sigma weight residual 1.524 1.541 -0.016 1.50e-02 4.44e+03 1.19e+00 bond pdb=" CA THR B 623 " pdb=" CB THR B 623 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.44e-02 4.82e+03 1.14e+00 bond pdb=" CA GLU A 527 " pdb=" C GLU A 527 " ideal model delta sigma weight residual 1.524 1.540 -0.015 1.50e-02 4.44e+03 1.06e+00 ... (remaining 10681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 14149 1.84 - 3.68: 286 3.68 - 5.53: 49 5.53 - 7.37: 26 7.37 - 9.21: 6 Bond angle restraints: 14516 Sorted by residual: angle pdb=" CA LEU B 514 " pdb=" CB LEU B 514 " pdb=" CG LEU B 514 " ideal model delta sigma weight residual 116.30 125.51 -9.21 3.50e+00 8.16e-02 6.93e+00 angle pdb=" CA LEU A 514 " pdb=" CB LEU A 514 " pdb=" CG LEU A 514 " ideal model delta sigma weight residual 116.30 125.49 -9.19 3.50e+00 8.16e-02 6.90e+00 angle pdb=" C PRO B 543 " pdb=" N ILE B 544 " pdb=" CA ILE B 544 " ideal model delta sigma weight residual 121.97 126.39 -4.42 1.80e+00 3.09e-01 6.04e+00 angle pdb=" C PRO A 543 " pdb=" N ILE A 544 " pdb=" CA ILE A 544 " ideal model delta sigma weight residual 121.97 126.35 -4.38 1.80e+00 3.09e-01 5.92e+00 angle pdb=" CB LEU B 401 " pdb=" CG LEU B 401 " pdb=" CD1 LEU B 401 " ideal model delta sigma weight residual 110.70 103.43 7.27 3.00e+00 1.11e-01 5.88e+00 ... (remaining 14511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 5693 17.46 - 34.93: 535 34.93 - 52.39: 90 52.39 - 69.86: 22 69.86 - 87.32: 4 Dihedral angle restraints: 6344 sinusoidal: 2442 harmonic: 3902 Sorted by residual: dihedral pdb=" CA LYS B 35 " pdb=" C LYS B 35 " pdb=" N ASP B 36 " pdb=" CA ASP B 36 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA LYS A 35 " pdb=" C LYS A 35 " pdb=" N ASP A 36 " pdb=" CA ASP A 36 " ideal model delta harmonic sigma weight residual 180.00 158.67 21.33 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA ALA B 525 " pdb=" C ALA B 525 " pdb=" N TYR B 526 " pdb=" CA TYR B 526 " ideal model delta harmonic sigma weight residual 180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 6341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1217 0.045 - 0.091: 409 0.091 - 0.136: 93 0.136 - 0.182: 7 0.182 - 0.227: 2 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CB ILE B 544 " pdb=" CA ILE B 544 " pdb=" CG1 ILE B 544 " pdb=" CG2 ILE B 544 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE A 544 " pdb=" CA ILE A 544 " pdb=" CG1 ILE A 544 " pdb=" CG2 ILE A 544 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA GLU B 527 " pdb=" N GLU B 527 " pdb=" C GLU B 527 " pdb=" CB GLU B 527 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 1725 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 542 " -0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO A 543 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 542 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO B 543 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 543 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 543 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 107 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.17e+00 pdb=" N PRO A 108 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " -0.020 5.00e-02 4.00e+02 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2731 2.80 - 3.33: 10639 3.33 - 3.85: 17632 3.85 - 4.38: 19419 4.38 - 4.90: 33508 Nonbonded interactions: 83929 Sorted by model distance: nonbonded pdb=" O LEU B 556 " pdb=" OG1 THR B 560 " model vdw 2.279 3.040 nonbonded pdb=" O LEU A 556 " pdb=" OG1 THR A 560 " model vdw 2.280 3.040 nonbonded pdb=" O SER B 86 " pdb=" OG1 THR B 90 " model vdw 2.317 3.040 nonbonded pdb=" O SER A 86 " pdb=" OG1 THR A 90 " model vdw 2.317 3.040 nonbonded pdb=" NH2 ARG B 150 " pdb=" OD2 ASP B 342 " model vdw 2.323 3.120 ... (remaining 83924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.50 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.770 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10686 Z= 0.212 Angle : 0.693 9.212 14516 Z= 0.343 Chirality : 0.046 0.227 1728 Planarity : 0.005 0.046 1804 Dihedral : 13.913 87.324 3840 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.67 (0.24), residues: 1338 helix: 1.08 (0.18), residues: 884 sheet: 3.81 (0.85), residues: 36 loop : -1.19 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 70 HIS 0.002 0.001 HIS A 17 PHE 0.014 0.001 PHE B 432 TYR 0.024 0.001 TYR A 114 ARG 0.005 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 380 ILE cc_start: 0.6264 (tp) cc_final: 0.6054 (tp) REVERT: A 428 THR cc_start: 0.7460 (m) cc_final: 0.7225 (p) REVERT: A 458 LEU cc_start: 0.8777 (mm) cc_final: 0.8573 (mm) REVERT: A 488 LEU cc_start: 0.8878 (tp) cc_final: 0.8582 (tp) REVERT: B 428 THR cc_start: 0.7473 (m) cc_final: 0.7269 (p) REVERT: B 458 LEU cc_start: 0.8775 (mm) cc_final: 0.8563 (mm) REVERT: B 488 LEU cc_start: 0.8887 (tp) cc_final: 0.8597 (tp) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1767 time to fit residues: 53.3436 Evaluate side-chains 156 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 54 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A 447 ASN B 48 GLN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN B 447 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10686 Z= 0.162 Angle : 0.566 6.054 14516 Z= 0.286 Chirality : 0.043 0.223 1728 Planarity : 0.004 0.046 1804 Dihedral : 4.217 20.596 1442 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.65 % Allowed : 8.43 % Favored : 89.91 % 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 (0.24), residues: 1338 helix: 1.44 (0.18), residues: 880 sheet: 4.12 (0.88), residues: 36 loop : -1.03 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 70 HIS 0.003 0.001 HIS B 640 PHE 0.010 0.001 PHE A 198 TYR 0.017 0.001 TYR A 545 ARG 0.002 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 1.183 Fit side-chains REVERT: A 237 TYR cc_start: 0.6549 (m-80) cc_final: 0.6346 (m-80) REVERT: A 458 LEU cc_start: 0.8799 (mm) cc_final: 0.8576 (mm) REVERT: A 488 LEU cc_start: 0.8820 (tp) cc_final: 0.8594 (tp) REVERT: B 458 LEU cc_start: 0.8776 (mm) cc_final: 0.8557 (mm) REVERT: B 488 LEU cc_start: 0.8800 (tp) cc_final: 0.8583 (tp) outliers start: 19 outliers final: 10 residues processed: 176 average time/residue: 0.1794 time to fit residues: 47.9109 Evaluate side-chains 159 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 633 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 97 optimal weight: 5.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10686 Z= 0.205 Angle : 0.565 6.884 14516 Z= 0.281 Chirality : 0.043 0.191 1728 Planarity : 0.004 0.048 1804 Dihedral : 4.108 19.559 1442 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.78 % Allowed : 11.91 % Favored : 85.30 % 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: 1.11 (0.24), residues: 1338 helix: 1.43 (0.18), residues: 896 sheet: 4.02 (0.84), residues: 36 loop : -1.13 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 472 HIS 0.006 0.001 HIS B 640 PHE 0.007 0.001 PHE B 391 TYR 0.011 0.001 TYR B 237 ARG 0.003 0.000 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 1.098 Fit side-chains REVERT: A 458 LEU cc_start: 0.8737 (mm) cc_final: 0.8489 (mm) REVERT: A 578 TYR cc_start: 0.6732 (t80) cc_final: 0.6166 (t80) REVERT: B 71 LEU cc_start: 0.8684 (mt) cc_final: 0.8467 (mt) REVERT: B 458 LEU cc_start: 0.8729 (mm) cc_final: 0.8480 (mm) outliers start: 32 outliers final: 18 residues processed: 180 average time/residue: 0.1753 time to fit residues: 48.1945 Evaluate side-chains 164 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 642 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10686 Z= 0.174 Angle : 0.541 7.015 14516 Z= 0.270 Chirality : 0.042 0.164 1728 Planarity : 0.004 0.048 1804 Dihedral : 4.072 19.037 1442 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.52 % Allowed : 14.09 % Favored : 83.39 % 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: 1.39 (0.24), residues: 1338 helix: 1.61 (0.18), residues: 880 sheet: 4.15 (0.84), residues: 36 loop : -0.84 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 70 HIS 0.004 0.001 HIS B 640 PHE 0.007 0.001 PHE B 391 TYR 0.017 0.001 TYR B 114 ARG 0.002 0.000 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: A 458 LEU cc_start: 0.8765 (mm) cc_final: 0.8515 (mm) REVERT: A 578 TYR cc_start: 0.6633 (t80) cc_final: 0.6102 (t80) REVERT: B 458 LEU cc_start: 0.8759 (mm) cc_final: 0.8489 (mm) REVERT: B 578 TYR cc_start: 0.6719 (t80) cc_final: 0.6215 (t80) outliers start: 29 outliers final: 22 residues processed: 174 average time/residue: 0.1792 time to fit residues: 47.6132 Evaluate side-chains 168 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 642 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN B 25 HIS ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 10686 Z= 0.452 Angle : 0.725 10.414 14516 Z= 0.364 Chirality : 0.049 0.225 1728 Planarity : 0.005 0.060 1804 Dihedral : 4.520 19.900 1442 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.30 % Allowed : 15.91 % Favored : 80.78 % 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: 0.64 (0.24), residues: 1338 helix: 1.06 (0.18), residues: 908 sheet: 4.01 (0.84), residues: 36 loop : -1.37 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 462 HIS 0.006 0.002 HIS A 640 PHE 0.011 0.002 PHE B 538 TYR 0.016 0.002 TYR B 340 ARG 0.004 0.001 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 1.228 Fit side-chains REVERT: A 415 CYS cc_start: 0.7363 (t) cc_final: 0.7075 (t) REVERT: A 451 MET cc_start: 0.8423 (mtp) cc_final: 0.8112 (mtp) REVERT: A 458 LEU cc_start: 0.8976 (mm) cc_final: 0.8612 (mm) REVERT: A 469 LEU cc_start: 0.8640 (tp) cc_final: 0.8438 (tp) REVERT: A 493 ILE cc_start: 0.8323 (mm) cc_final: 0.8094 (mt) REVERT: A 518 ASP cc_start: 0.7875 (t0) cc_final: 0.7595 (t0) REVERT: A 578 TYR cc_start: 0.6674 (t80) cc_final: 0.6436 (t80) REVERT: B 294 PHE cc_start: 0.7608 (t80) cc_final: 0.7408 (t80) REVERT: B 451 MET cc_start: 0.8426 (mtp) cc_final: 0.8116 (mtp) REVERT: B 458 LEU cc_start: 0.8959 (mm) cc_final: 0.8612 (mm) REVERT: B 493 ILE cc_start: 0.8309 (mm) cc_final: 0.8078 (mt) REVERT: B 578 TYR cc_start: 0.6756 (t80) cc_final: 0.6414 (t80) outliers start: 38 outliers final: 26 residues processed: 172 average time/residue: 0.1793 time to fit residues: 47.1468 Evaluate side-chains 160 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 545 TYR Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 642 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.1980 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 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 25 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS B 308 ASN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10686 Z= 0.159 Angle : 0.566 8.743 14516 Z= 0.282 Chirality : 0.043 0.151 1728 Planarity : 0.005 0.055 1804 Dihedral : 4.285 18.675 1442 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.78 % Allowed : 18.61 % Favored : 78.61 % 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: 1.01 (0.24), residues: 1338 helix: 1.34 (0.18), residues: 908 sheet: 3.93 (0.85), residues: 36 loop : -1.22 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 70 HIS 0.002 0.001 HIS A 17 PHE 0.024 0.001 PHE A 294 TYR 0.011 0.001 TYR A 237 ARG 0.002 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 156 time to evaluate : 1.171 Fit side-chains REVERT: A 225 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7669 (mpp) REVERT: A 294 PHE cc_start: 0.8120 (t80) cc_final: 0.7466 (t80) REVERT: A 415 CYS cc_start: 0.7170 (t) cc_final: 0.6818 (t) REVERT: A 458 LEU cc_start: 0.8881 (mm) cc_final: 0.8633 (mm) REVERT: A 578 TYR cc_start: 0.6764 (t80) cc_final: 0.6444 (t80) REVERT: B 225 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7670 (mpp) REVERT: B 340 TYR cc_start: 0.5947 (OUTLIER) cc_final: 0.4121 (m-80) REVERT: B 458 LEU cc_start: 0.8855 (mm) cc_final: 0.8643 (mm) REVERT: B 578 TYR cc_start: 0.6654 (t80) cc_final: 0.6375 (t80) REVERT: B 653 ASP cc_start: 0.8279 (m-30) cc_final: 0.8016 (m-30) outliers start: 32 outliers final: 25 residues processed: 174 average time/residue: 0.1833 time to fit residues: 47.8286 Evaluate side-chains 169 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 643 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 72 optimal weight: 0.0270 chunk 129 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10686 Z= 0.206 Angle : 0.586 8.795 14516 Z= 0.287 Chirality : 0.043 0.163 1728 Planarity : 0.004 0.052 1804 Dihedral : 4.201 17.861 1442 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.74 % Allowed : 18.09 % Favored : 78.17 % 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 (0.24), residues: 1338 helix: 1.43 (0.18), residues: 910 sheet: 4.00 (0.83), residues: 36 loop : -1.22 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 70 HIS 0.003 0.001 HIS B 640 PHE 0.024 0.001 PHE B 294 TYR 0.011 0.001 TYR B 114 ARG 0.002 0.000 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 144 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7718 (mpp) REVERT: A 294 PHE cc_start: 0.8144 (t80) cc_final: 0.7498 (t80) REVERT: A 458 LEU cc_start: 0.8844 (mm) cc_final: 0.8542 (mm) REVERT: A 578 TYR cc_start: 0.6815 (t80) cc_final: 0.6474 (t80) REVERT: B 222 PHE cc_start: 0.7251 (t80) cc_final: 0.6512 (m-80) REVERT: B 225 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7670 (mpp) REVERT: B 273 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8013 (mp) REVERT: B 340 TYR cc_start: 0.5885 (OUTLIER) cc_final: 0.4150 (m-80) REVERT: B 458 LEU cc_start: 0.8843 (mm) cc_final: 0.8568 (mm) REVERT: B 578 TYR cc_start: 0.6631 (t80) cc_final: 0.6365 (t80) REVERT: B 653 ASP cc_start: 0.8251 (m-30) cc_final: 0.7834 (m-30) outliers start: 43 outliers final: 25 residues processed: 169 average time/residue: 0.1747 time to fit residues: 44.9857 Evaluate side-chains 163 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 643 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 0.029 10686 Z= 0.167 Angle : 0.558 8.291 14516 Z= 0.276 Chirality : 0.043 0.198 1728 Planarity : 0.004 0.048 1804 Dihedral : 4.144 17.258 1442 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.96 % Allowed : 18.26 % Favored : 78.78 % 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: 1.39 (0.24), residues: 1338 helix: 1.62 (0.18), residues: 896 sheet: 4.05 (0.84), residues: 36 loop : -0.96 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 70 HIS 0.002 0.001 HIS B 17 PHE 0.015 0.001 PHE A 294 TYR 0.009 0.001 TYR A 237 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 1.155 Fit side-chains REVERT: A 225 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7641 (mpp) REVERT: A 294 PHE cc_start: 0.8159 (t80) cc_final: 0.7540 (t80) REVERT: A 458 LEU cc_start: 0.8845 (mm) cc_final: 0.8586 (mm) REVERT: A 578 TYR cc_start: 0.6806 (t80) cc_final: 0.6457 (t80) REVERT: A 653 ASP cc_start: 0.7982 (m-30) cc_final: 0.7659 (m-30) REVERT: B 222 PHE cc_start: 0.7271 (t80) cc_final: 0.6501 (m-80) REVERT: B 225 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7633 (mpp) REVERT: B 273 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7998 (mp) REVERT: B 294 PHE cc_start: 0.7991 (t80) cc_final: 0.7446 (t80) REVERT: B 458 LEU cc_start: 0.8832 (mm) cc_final: 0.8572 (mm) REVERT: B 578 TYR cc_start: 0.6621 (t80) cc_final: 0.6346 (t80) REVERT: B 653 ASP cc_start: 0.8161 (m-30) cc_final: 0.7888 (m-30) outliers start: 34 outliers final: 24 residues processed: 162 average time/residue: 0.1618 time to fit residues: 40.8114 Evaluate side-chains 161 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 643 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 0.0050 chunk 36 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10686 Z= 0.185 Angle : 0.575 9.191 14516 Z= 0.281 Chirality : 0.043 0.200 1728 Planarity : 0.004 0.048 1804 Dihedral : 4.113 16.906 1442 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.13 % Allowed : 18.61 % Favored : 78.26 % 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: 1.41 (0.24), residues: 1338 helix: 1.64 (0.18), residues: 896 sheet: 4.12 (0.83), residues: 36 loop : -0.95 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 70 HIS 0.003 0.001 HIS A 640 PHE 0.014 0.001 PHE A 294 TYR 0.024 0.001 TYR A 114 ARG 0.002 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.167 Fit side-chains REVERT: A 225 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7675 (mpp) REVERT: A 294 PHE cc_start: 0.8224 (t80) cc_final: 0.7619 (t80) REVERT: A 458 LEU cc_start: 0.8826 (mm) cc_final: 0.8528 (mm) REVERT: A 578 TYR cc_start: 0.6807 (t80) cc_final: 0.6461 (t80) REVERT: B 222 PHE cc_start: 0.7235 (t80) cc_final: 0.6428 (m-80) REVERT: B 225 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7684 (mpp) REVERT: B 273 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8008 (mp) REVERT: B 294 PHE cc_start: 0.8169 (t80) cc_final: 0.7641 (t80) REVERT: B 458 LEU cc_start: 0.8785 (mm) cc_final: 0.8554 (mm) REVERT: B 578 TYR cc_start: 0.6644 (t80) cc_final: 0.6364 (t80) REVERT: B 653 ASP cc_start: 0.8126 (m-30) cc_final: 0.7894 (m-30) outliers start: 36 outliers final: 28 residues processed: 157 average time/residue: 0.1689 time to fit residues: 41.1612 Evaluate side-chains 166 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 643 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10686 Z= 0.197 Angle : 0.571 8.591 14516 Z= 0.282 Chirality : 0.043 0.209 1728 Planarity : 0.004 0.049 1804 Dihedral : 4.136 16.795 1442 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.13 % Allowed : 18.43 % Favored : 78.43 % 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: 1.43 (0.24), residues: 1338 helix: 1.65 (0.18), residues: 894 sheet: 4.12 (0.83), residues: 36 loop : -0.92 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 70 HIS 0.003 0.001 HIS A 640 PHE 0.013 0.001 PHE A 294 TYR 0.022 0.001 TYR B 114 ARG 0.001 0.000 ARG A 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.153 Fit side-chains REVERT: A 222 PHE cc_start: 0.7044 (t80) cc_final: 0.6533 (m-80) REVERT: A 225 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7673 (mpp) REVERT: A 294 PHE cc_start: 0.8203 (t80) cc_final: 0.7614 (t80) REVERT: A 458 LEU cc_start: 0.8806 (mm) cc_final: 0.8518 (mm) REVERT: A 518 ASP cc_start: 0.7475 (t0) cc_final: 0.7218 (t0) REVERT: A 578 TYR cc_start: 0.6807 (t80) cc_final: 0.6461 (t80) REVERT: A 653 ASP cc_start: 0.8096 (m-30) cc_final: 0.7805 (m-30) REVERT: B 222 PHE cc_start: 0.7024 (t80) cc_final: 0.6439 (m-80) REVERT: B 225 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7696 (mpp) REVERT: B 273 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7987 (mp) REVERT: B 294 PHE cc_start: 0.8116 (t80) cc_final: 0.7586 (t80) REVERT: B 458 LEU cc_start: 0.8787 (mm) cc_final: 0.8527 (mm) REVERT: B 578 TYR cc_start: 0.6718 (t80) cc_final: 0.6428 (t80) REVERT: B 653 ASP cc_start: 0.8136 (m-30) cc_final: 0.7866 (m-30) outliers start: 36 outliers final: 27 residues processed: 162 average time/residue: 0.1664 time to fit residues: 42.3841 Evaluate side-chains 170 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 643 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 6 optimal weight: 0.0870 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 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 = 0.3566 r_free = 0.3566 target = 0.118868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.095568 restraints weight = 20084.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097848 restraints weight = 11191.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099205 restraints weight = 7881.819| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10686 Z= 0.159 Angle : 0.565 8.887 14516 Z= 0.276 Chirality : 0.043 0.191 1728 Planarity : 0.004 0.049 1804 Dihedral : 4.106 16.442 1442 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.17 % Allowed : 19.91 % Favored : 77.91 % 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: 1.44 (0.24), residues: 1338 helix: 1.64 (0.18), residues: 898 sheet: 4.16 (0.83), residues: 36 loop : -0.90 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 70 HIS 0.003 0.001 HIS B 220 PHE 0.013 0.001 PHE A 294 TYR 0.009 0.001 TYR B 228 ARG 0.001 0.000 ARG A 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1930.40 seconds wall clock time: 35 minutes 32.67 seconds (2132.67 seconds total)