Starting phenix.real_space_refine on Tue Nov 14 06:18:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln5_0924/11_2023/6ln5_0924_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln5_0924/11_2023/6ln5_0924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln5_0924/11_2023/6ln5_0924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln5_0924/11_2023/6ln5_0924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln5_0924/11_2023/6ln5_0924_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln5_0924/11_2023/6ln5_0924_updated.pdb" } resolution = 2.8 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= 0.011 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 3 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 4988 2.51 5 N 1311 2.21 5 O 1478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A ASP 375": "OD1" <-> "OD2" Residue "A ASP 408": "OD1" <-> "OD2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A ASP 456": "OD1" <-> "OD2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 587": "OE1" <-> "OE2" Residue "A ASP 644": "OD1" <-> "OD2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 886": "OD1" <-> "OD2" Residue "A GLU 950": "OE1" <-> "OE2" Residue "A ASP 980": "OD1" <-> "OD2" Residue "A GLU 981": "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: 7840 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7840 Unusual residues: {' CA': 2, ' MG': 1, 'ACP': 1} Classifications: {'peptide': 1011, 'undetermined': 4} Link IDs: {'PTRANS': 46, 'TRANS': 964, None: 4} Not linked: pdbres="SER A1031 " pdbres="ACP A2001 " Not linked: pdbres="ACP A2001 " pdbres=" MG A2002 " Not linked: pdbres=" MG A2002 " pdbres=" CA A2003 " Not linked: pdbres=" CA A2003 " pdbres=" CA A2004 " Chain breaks: 1 Time building chain proxies: 4.77, per 1000 atoms: 0.61 Number of scatterers: 7840 At special positions: 0 Unit cell: (103.335, 79.68, 138.195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 57 16.00 P 3 15.00 Mg 1 11.99 O 1478 8.00 N 1311 7.00 C 4988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 875 " - pdb=" SG CYS A 887 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.5 seconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 7 sheets defined 46.8% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 49 through 58 removed outlier: 4.227A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 77 removed outlier: 3.955A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 119 removed outlier: 3.500A pdb=" N ILE A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 248 through 273 removed outlier: 3.545A pdb=" N LYS A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 288 through 306 Processing helix chain 'A' and resid 311 through 328 removed outlier: 3.614A pdb=" N THR A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 4.369A pdb=" N GLU A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N CYS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 408 through 419 Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.833A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.556A pdb=" N LYS A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 586 No H-bonds generated for 'chain 'A' and resid 583 through 586' Processing helix chain 'A' and resid 604 through 615 removed outlier: 4.600A pdb=" N SER A 608 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 662 through 669 removed outlier: 3.732A pdb=" N ASP A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 693 removed outlier: 3.626A pdb=" N SER A 684 " --> pdb=" O PRO A 680 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 712 removed outlier: 3.507A pdb=" N ALA A 707 " --> pdb=" O VAL A 704 " (cutoff:3.500A) Proline residue: A 708 - end of helix removed outlier: 3.569A pdb=" N LYS A 711 " --> pdb=" O PRO A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 728 Processing helix chain 'A' and resid 739 through 780 removed outlier: 3.537A pdb=" N VAL A 743 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 747 " --> pdb=" O ALA A 744 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 748 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 750 " --> pdb=" O GLU A 747 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 752 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 753 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 755 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 758 " --> pdb=" O ASN A 755 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 764 " --> pdb=" O ARG A 761 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER A 765 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER A 766 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN A 767 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL A 768 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 772 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS A 773 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 776 " --> pdb=" O CYS A 773 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 777 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 798 Processing helix chain 'A' and resid 801 through 808 removed outlier: 4.409A pdb=" N LEU A 806 " --> pdb=" O PRO A 802 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY A 807 " --> pdb=" O ALA A 803 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.637A pdb=" N TYR A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 851 " --> pdb=" O THR A 847 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 872 through 874 No H-bonds generated for 'chain 'A' and resid 872 through 874' Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 893 through 912 Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 930 through 948 Processing helix chain 'A' and resid 952 through 955 No H-bonds generated for 'chain 'A' and resid 952 through 955' Processing helix chain 'A' and resid 963 through 989 Proline residue: A 975 - end of helix removed outlier: 3.791A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1030 Proline residue: A1024 - end of helix removed outlier: 3.593A pdb=" N TRP A1028 " --> pdb=" O PRO A1024 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 138 through 141 removed outlier: 4.366A pdb=" N LYS A 128 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE A 150 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.700A pdb=" N LEU A 173 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP A 176 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE A 214 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 331 through 333 removed outlier: 6.679A pdb=" N VAL A 347 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N THR A 700 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS A 349 " --> pdb=" O THR A 700 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG A 619 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N SER A 350 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 621 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 424 through 428 Processing sheet with id= E, first strand: chain 'A' and resid 377 through 383 removed outlier: 5.318A pdb=" N ASN A 380 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU A 369 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE A 382 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N PHE A 367 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY A 597 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N MET A 366 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N CYS A 595 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE A 368 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N VAL A 593 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 13.145A pdb=" N ASP A 370 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 16.326A pdb=" N THR A 591 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 483 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 532 through 535 removed outlier: 6.998A pdb=" N LEU A 590 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE A 527 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE A 592 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL A 529 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.554A pdb=" N CYS A 674 " --> pdb=" O PHE A 652 " (cutoff:3.500A) No H-bonds generated for sheet with id= G 327 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2575 1.35 - 1.48: 1793 1.48 - 1.61: 3523 1.61 - 1.73: 4 1.73 - 1.86: 90 Bond restraints: 7985 Sorted by residual: bond pdb=" C1' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.390 1.618 -0.228 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C1' ACP A2001 " pdb=" C2' ACP A2001 " ideal model delta sigma weight residual 1.527 1.307 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C4' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.428 1.302 0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 1.335 1.449 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C2' ACP A2001 " pdb=" O2' ACP A2001 " ideal model delta sigma weight residual 1.401 1.493 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 7980 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.77: 245 106.77 - 113.57: 4540 113.57 - 120.36: 2875 120.36 - 127.16: 3096 127.16 - 133.96: 88 Bond angle restraints: 10844 Sorted by residual: angle pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O5' ACP A2001 " ideal model delta sigma weight residual 93.75 109.29 -15.54 3.00e+00 1.11e-01 2.68e+01 angle pdb=" C3B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O3A ACP A2001 " ideal model delta sigma weight residual 98.05 110.00 -11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" N1 ACP A2001 " pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 119.32 108.11 11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" O1B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O2B ACP A2001 " ideal model delta sigma weight residual 119.60 109.01 10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O1A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O2A ACP A2001 " ideal model delta sigma weight residual 118.95 108.61 10.34 3.00e+00 1.11e-01 1.19e+01 ... (remaining 10839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.94: 4603 21.94 - 43.89: 205 43.89 - 65.83: 13 65.83 - 87.78: 10 87.78 - 109.72: 2 Dihedral angle restraints: 4833 sinusoidal: 1913 harmonic: 2920 Sorted by residual: dihedral pdb=" CA CYS A 887 " pdb=" C CYS A 887 " pdb=" N ALA A 888 " pdb=" CA ALA A 888 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" O1A ACP A2001 " pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" PB ACP A2001 " ideal model delta sinusoidal sigma weight residual -48.75 60.97 -109.72 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" CA PRO A 951 " pdb=" C PRO A 951 " pdb=" N LEU A 952 " pdb=" CA LEU A 952 " ideal model delta harmonic sigma weight residual -180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1177 0.077 - 0.154: 95 0.154 - 0.231: 0 0.231 - 0.308: 0 0.308 - 0.385: 1 Chirality restraints: 1273 Sorted by residual: chirality pdb=" C2' ACP A2001 " pdb=" C1' ACP A2001 " pdb=" C3' ACP A2001 " pdb=" O2' ACP A2001 " both_signs ideal model delta sigma weight residual False -2.75 -2.37 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA ILE A 623 " pdb=" N ILE A 623 " pdb=" C ILE A 623 " pdb=" CB ILE A 623 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA VAL A 437 " pdb=" N VAL A 437 " pdb=" C VAL A 437 " pdb=" CB VAL A 437 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 1270 not shown) Planarity restraints: 1377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A1016 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A1017 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A1017 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1017 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 975 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 787 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 788 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 788 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 788 " 0.020 5.00e-02 4.00e+02 ... (remaining 1374 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 76 2.60 - 3.18: 6684 3.18 - 3.75: 12079 3.75 - 4.33: 17865 4.33 - 4.90: 29018 Nonbonded interactions: 65722 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.027 2.170 nonbonded pdb=" OE2 GLU A 309 " pdb=" OD1 ASN A 795 " model vdw 2.027 3.040 nonbonded pdb=" O ILE A 307 " pdb=" OE1 GLU A 309 " model vdw 2.161 3.040 nonbonded pdb=" OD1 ASP A 702 " pdb="MG MG A2002 " model vdw 2.172 2.170 nonbonded pdb=" NH1 ARG A 491 " pdb=" OE2 GLU A 587 " model vdw 2.212 2.520 ... (remaining 65717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 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: 1.460 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 26.040 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.005 0.228 7985 Z= 0.318 Angle : 0.630 15.544 10844 Z= 0.335 Chirality : 0.042 0.385 1273 Planarity : 0.004 0.039 1377 Dihedral : 12.322 109.724 2938 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.20), residues: 1007 helix: -3.50 (0.13), residues: 500 sheet: -1.77 (0.40), residues: 132 loop : -1.65 (0.27), residues: 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 1.003 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 1.4273 time to fit residues: 250.6878 Evaluate side-chains 118 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.2692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN A 874 GLN A 913 ASN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7985 Z= 0.202 Angle : 0.511 6.039 10844 Z= 0.265 Chirality : 0.042 0.130 1273 Planarity : 0.005 0.041 1377 Dihedral : 6.466 143.638 1075 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.01 % Allowed : 11.34 % Favored : 85.65 % 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: -1.86 (0.24), residues: 1007 helix: -1.04 (0.21), residues: 501 sheet: -1.25 (0.42), residues: 136 loop : -1.22 (0.29), residues: 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.890 Fit side-chains outliers start: 26 outliers final: 10 residues processed: 134 average time/residue: 1.3194 time to fit residues: 186.8671 Evaluate side-chains 119 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.1188 time to fit residues: 2.0075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN A 874 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7985 Z= 0.181 Angle : 0.486 5.959 10844 Z= 0.249 Chirality : 0.041 0.127 1273 Planarity : 0.004 0.040 1377 Dihedral : 6.482 146.425 1075 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.78 % Allowed : 14.93 % Favored : 82.29 % 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: -0.80 (0.25), residues: 1007 helix: 0.03 (0.23), residues: 501 sheet: -1.20 (0.43), residues: 124 loop : -0.87 (0.30), residues: 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.955 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 129 average time/residue: 1.3154 time to fit residues: 179.3767 Evaluate side-chains 120 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.0852 time to fit residues: 1.8485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 0.0570 chunk 26 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN A 874 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7985 Z= 0.164 Angle : 0.478 5.911 10844 Z= 0.243 Chirality : 0.041 0.138 1273 Planarity : 0.004 0.039 1377 Dihedral : 6.402 145.351 1075 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.55 % Allowed : 15.05 % Favored : 82.41 % 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: -0.19 (0.26), residues: 1007 helix: 0.60 (0.24), residues: 496 sheet: -0.86 (0.42), residues: 136 loop : -0.67 (0.31), residues: 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 1.010 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 121 average time/residue: 1.4494 time to fit residues: 184.5264 Evaluate side-chains 117 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 0.3135 time to fit residues: 3.1392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 0.0050 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN A 874 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7985 Z= 0.233 Angle : 0.520 6.085 10844 Z= 0.263 Chirality : 0.043 0.140 1273 Planarity : 0.004 0.038 1377 Dihedral : 6.865 158.573 1075 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.01 % Allowed : 15.97 % Favored : 81.02 % 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: -0.04 (0.26), residues: 1007 helix: 0.66 (0.24), residues: 503 sheet: -0.76 (0.42), residues: 136 loop : -0.53 (0.31), residues: 368 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.978 Fit side-chains outliers start: 26 outliers final: 15 residues processed: 123 average time/residue: 1.4966 time to fit residues: 194.6954 Evaluate side-chains 119 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 0.1150 time to fit residues: 2.2398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.0870 chunk 19 optimal weight: 0.3980 chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 0.2980 chunk 97 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7985 Z= 0.135 Angle : 0.470 5.789 10844 Z= 0.237 Chirality : 0.040 0.129 1273 Planarity : 0.004 0.035 1377 Dihedral : 6.558 153.841 1075 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.20 % Allowed : 17.48 % Favored : 80.32 % 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: 0.36 (0.27), residues: 1007 helix: 1.03 (0.24), residues: 496 sheet: -0.79 (0.44), residues: 124 loop : -0.30 (0.31), residues: 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.891 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 120 average time/residue: 1.3416 time to fit residues: 170.1463 Evaluate side-chains 109 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.0819 time to fit residues: 1.5908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7985 Z= 0.228 Angle : 0.524 6.762 10844 Z= 0.263 Chirality : 0.043 0.134 1273 Planarity : 0.004 0.034 1377 Dihedral : 6.911 162.213 1075 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.43 % Allowed : 17.71 % Favored : 79.86 % 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: 0.27 (0.27), residues: 1007 helix: 0.89 (0.24), residues: 503 sheet: -0.65 (0.42), residues: 136 loop : -0.32 (0.32), residues: 368 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 0.922 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 118 average time/residue: 1.3019 time to fit residues: 162.6257 Evaluate side-chains 113 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.0739 time to fit residues: 1.6278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7985 Z= 0.191 Angle : 0.508 6.763 10844 Z= 0.255 Chirality : 0.042 0.130 1273 Planarity : 0.004 0.033 1377 Dihedral : 6.980 165.977 1075 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.85 % Allowed : 18.52 % Favored : 79.63 % 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: 0.34 (0.27), residues: 1007 helix: 0.94 (0.24), residues: 504 sheet: -0.66 (0.42), residues: 136 loop : -0.25 (0.32), residues: 367 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.934 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 120 average time/residue: 1.4379 time to fit residues: 182.5972 Evaluate side-chains 114 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.0819 time to fit residues: 1.5041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 0.0370 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7985 Z= 0.196 Angle : 0.515 7.126 10844 Z= 0.258 Chirality : 0.042 0.131 1273 Planarity : 0.004 0.033 1377 Dihedral : 7.081 169.056 1075 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.85 % Allowed : 18.63 % Favored : 79.51 % 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: 0.37 (0.27), residues: 1007 helix: 0.97 (0.24), residues: 504 sheet: -0.64 (0.43), residues: 136 loop : -0.24 (0.32), residues: 367 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.207 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 119 average time/residue: 1.3096 time to fit residues: 164.9011 Evaluate side-chains 115 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.0723 time to fit residues: 1.3206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 80 optimal weight: 0.4980 chunk 8 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7985 Z= 0.179 Angle : 0.506 7.364 10844 Z= 0.253 Chirality : 0.042 0.129 1273 Planarity : 0.004 0.035 1377 Dihedral : 7.114 171.517 1075 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.85 % Allowed : 18.98 % Favored : 79.17 % 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: 0.44 (0.27), residues: 1007 helix: 1.03 (0.24), residues: 503 sheet: -0.78 (0.44), residues: 124 loop : -0.16 (0.32), residues: 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.949 Fit side-chains outliers start: 16 outliers final: 15 residues processed: 116 average time/residue: 1.3710 time to fit residues: 168.2980 Evaluate side-chains 115 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.1731 time to fit residues: 1.9260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.0270 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.107322 restraints weight = 8957.591| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.56 r_work: 0.2992 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7985 Z= 0.134 Angle : 0.485 8.284 10844 Z= 0.241 Chirality : 0.041 0.127 1273 Planarity : 0.004 0.032 1377 Dihedral : 6.936 169.605 1075 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.85 % Allowed : 18.87 % Favored : 79.28 % 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: 0.73 (0.27), residues: 1007 helix: 1.30 (0.24), residues: 497 sheet: -0.63 (0.44), residues: 123 loop : -0.08 (0.32), residues: 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3487.92 seconds wall clock time: 62 minutes 40.63 seconds (3760.63 seconds total)