Starting phenix.real_space_refine on Wed Nov 15 03:24:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sun_25442/11_2023/7sun_25442.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sun_25442/11_2023/7sun_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_25442/11_2023/7sun_25442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sun_25442/11_2023/7sun_25442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sun_25442/11_2023/7sun_25442.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sun_25442/11_2023/7sun_25442.pdb" } 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 Residue "A TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 637": "OE1" <-> "OE2" Residue "B TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 637": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 10454 Number of models: 1 Model: "" Number of chains: 2 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 Chain: "B" 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 Time building chain proxies: 5.61, per 1000 atoms: 0.54 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 - 3.50 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: 4.09 Conformation dependent library (CDL) restraints added in 1.9 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: 1.09 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: 3.28 Time building geometry restraints manager: 4.44 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: 99.42 - 106.33: 306 106.33 - 113.24: 5901 113.24 - 120.16: 3757 120.16 - 127.07: 4457 127.07 - 133.98: 95 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 2.440 nonbonded pdb=" O LEU A 556 " pdb=" OG1 THR A 560 " model vdw 2.280 2.440 nonbonded pdb=" O SER B 86 " pdb=" OG1 THR B 90 " model vdw 2.317 2.440 nonbonded pdb=" O SER A 86 " pdb=" OG1 THR A 90 " model vdw 2.317 2.440 nonbonded pdb=" NH2 ARG B 150 " pdb=" OD2 ASP B 342 " model vdw 2.323 2.520 ... (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 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: 0.700 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: 3.570 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 30.050 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.940 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.130 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1819 time to fit residues: 54.9959 Evaluate side-chains 154 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5521 ------------------------------------------------------------------------------- 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: 0.3980 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 121 optimal weight: 0.0060 overall best weight: 0.4154 ------------------------------------------------------------------------------- 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 447 ASN B 48 GLN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10686 Z= 0.144 Angle : 0.547 5.728 14516 Z= 0.275 Chirality : 0.042 0.220 1728 Planarity : 0.004 0.045 1804 Dihedral : 4.180 20.786 1442 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.09 % Allowed : 8.26 % Favored : 89.65 % 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: 1.46 (0.18), residues: 880 sheet: 4.01 (0.87), residues: 36 loop : -1.07 (0.31), residues: 422 *********************** 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 187 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.251 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 171 average time/residue: 0.1814 time to fit residues: 47.4989 Evaluate side-chains 158 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1048 time to fit residues: 3.8711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 120 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 389 GLN A 650 ASN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10686 Z= 0.289 Angle : 0.611 7.554 14516 Z= 0.305 Chirality : 0.045 0.225 1728 Planarity : 0.005 0.052 1804 Dihedral : 4.209 19.912 1442 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.61 % Allowed : 12.87 % Favored : 84.52 % 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: 0.95 (0.24), residues: 1338 helix: 1.31 (0.18), residues: 908 sheet: 4.21 (0.83), residues: 36 loop : -1.32 (0.32), residues: 394 *********************** 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 185 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 1.175 Fit side-chains outliers start: 30 outliers final: 17 residues processed: 173 average time/residue: 0.1878 time to fit residues: 50.7763 Evaluate side-chains 155 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0997 time to fit residues: 4.7998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7814 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10686 Z= 0.166 Angle : 0.537 7.022 14516 Z= 0.268 Chirality : 0.043 0.158 1728 Planarity : 0.004 0.050 1804 Dihedral : 4.130 19.425 1442 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.39 % Allowed : 15.04 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.24), residues: 1338 helix: 1.45 (0.18), residues: 896 sheet: 4.44 (0.84), residues: 36 loop : -1.07 (0.32), residues: 406 *********************** 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 171 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 1.297 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 158 average time/residue: 0.1846 time to fit residues: 45.0427 Evaluate side-chains 145 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 1.273 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0987 time to fit residues: 2.6597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 89 optimal weight: 0.0670 chunk 0 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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: 0.7865 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10686 Z= 0.236 Angle : 0.579 7.914 14516 Z= 0.285 Chirality : 0.044 0.176 1728 Planarity : 0.004 0.053 1804 Dihedral : 4.134 18.655 1442 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.91 % Allowed : 16.52 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1338 helix: 1.46 (0.18), residues: 906 sheet: 4.42 (0.83), residues: 36 loop : -1.21 (0.32), residues: 396 *********************** 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 169 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 1.220 Fit side-chains outliers start: 22 outliers final: 10 residues processed: 157 average time/residue: 0.1793 time to fit residues: 43.3359 Evaluate side-chains 144 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 1.645 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1032 time to fit residues: 3.5545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 76 optimal weight: 0.0470 chunk 31 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- 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: 0.7832 moved from start: 0.2221 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= 0.165 Angle : 0.537 7.426 14516 Z= 0.266 Chirality : 0.042 0.156 1728 Planarity : 0.004 0.051 1804 Dihedral : 4.067 17.775 1442 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.87 % Allowed : 18.35 % 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: 1.40 (0.24), residues: 1338 helix: 1.66 (0.18), residues: 880 sheet: 4.42 (0.84), residues: 36 loop : -0.96 (0.32), residues: 422 *********************** 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 160 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.236 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 152 average time/residue: 0.1843 time to fit residues: 42.8356 Evaluate side-chains 136 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0964 time to fit residues: 2.4020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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: 0.7882 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10686 Z= 0.257 Angle : 0.590 8.175 14516 Z= 0.292 Chirality : 0.045 0.211 1728 Planarity : 0.005 0.054 1804 Dihedral : 4.147 17.283 1442 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.26 % Allowed : 18.00 % Favored : 79.74 % 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: 1.21 (0.24), residues: 1338 helix: 1.48 (0.18), residues: 902 sheet: 4.48 (0.84), residues: 36 loop : -1.12 (0.32), residues: 400 *********************** 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 164 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.148 Fit side-chains outliers start: 26 outliers final: 12 residues processed: 150 average time/residue: 0.1776 time to fit residues: 41.4103 Evaluate side-chains 141 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1041 time to fit residues: 3.8873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** 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: 0.7863 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10686 Z= 0.210 Angle : 0.574 8.032 14516 Z= 0.284 Chirality : 0.044 0.236 1728 Planarity : 0.004 0.056 1804 Dihedral : 4.126 17.358 1442 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.30 % Allowed : 19.39 % Favored : 79.30 % 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: 1.37 (0.24), residues: 1338 helix: 1.61 (0.18), residues: 878 sheet: 4.46 (0.85), residues: 36 loop : -0.90 (0.32), residues: 424 *********************** 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 150 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.370 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 141 average time/residue: 0.1982 time to fit residues: 43.3435 Evaluate side-chains 138 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1028 time to fit residues: 3.2410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** 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: 0.7832 moved from start: 0.2525 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= 0.161 Angle : 0.544 7.455 14516 Z= 0.269 Chirality : 0.043 0.211 1728 Planarity : 0.004 0.056 1804 Dihedral : 4.025 16.281 1442 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.61 % Allowed : 19.91 % Favored : 79.48 % 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: 1.47 (0.25), residues: 1338 helix: 1.70 (0.18), residues: 878 sheet: 4.49 (0.85), residues: 36 loop : -0.91 (0.32), residues: 424 *********************** 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 153 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 1.244 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 149 average time/residue: 0.1856 time to fit residues: 42.1718 Evaluate side-chains 139 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 1.265 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1141 time to fit residues: 2.5585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 84 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.7834 moved from start: 0.2584 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= 0.176 Angle : 0.575 8.532 14516 Z= 0.278 Chirality : 0.044 0.287 1728 Planarity : 0.004 0.056 1804 Dihedral : 4.032 16.209 1442 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.26 % Allowed : 20.35 % Favored : 79.39 % 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: 1.59 (0.24), residues: 1338 helix: 1.81 (0.18), residues: 862 sheet: 4.33 (0.82), residues: 36 loop : -0.77 (0.32), residues: 440 ********************** 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 142 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 1.683 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 139 average time/residue: 0.1887 time to fit residues: 40.3716 Evaluate side-chains 135 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.215 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.7980 chunk 98 optimal weight: 0.0030 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.097844 restraints weight = 20139.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100119 restraints weight = 11066.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101516 restraints weight = 7722.984| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10686 Z= 0.150 Angle : 0.545 7.047 14516 Z= 0.268 Chirality : 0.043 0.256 1728 Planarity : 0.004 0.056 1804 Dihedral : 4.019 17.529 1442 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.26 % Allowed : 20.70 % Favored : 79.04 % 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: 1.58 (0.24), residues: 1338 helix: 1.76 (0.18), residues: 876 sheet: 4.51 (0.80), residues: 36 loop : -0.78 (0.32), residues: 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1954.68 seconds wall clock time: 37 minutes 6.15 seconds (2226.15 seconds total)