Starting phenix.real_space_refine on Fri Dec 8 08:44:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln6_0925/12_2023/6ln6_0925_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln6_0925/12_2023/6ln6_0925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln6_0925/12_2023/6ln6_0925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln6_0925/12_2023/6ln6_0925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln6_0925/12_2023/6ln6_0925_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln6_0925/12_2023/6ln6_0925_updated.pdb" } resolution = 2.9 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= 0.013 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 4986 2.51 5 N 1310 2.21 5 O 1477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ASP 281": "OD1" <-> "OD2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A GLU 550": "OE1" <-> "OE2" Residue "A GLU 587": "OE1" <-> "OE2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "A ASP 658": "OD1" <-> "OD2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A GLU 907": "OE1" <-> "OE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7836 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7836 Unusual residues: {' CA': 2, ' MG': 1, 'ACP': 1} Classifications: {'peptide': 1010, 'undetermined': 4} Link IDs: {'PTRANS': 46, 'TRANS': 963, 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: 4.67, per 1000 atoms: 0.60 Number of scatterers: 7836 At special positions: 0 Unit cell: (103.335, 79.68, 140.685, 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 1477 8.00 N 1310 7.00 C 4986 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: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 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 8 sheets defined 47.1% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 removed outlier: 4.101A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 49 through 56 removed outlier: 3.773A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 77 removed outlier: 3.740A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 119 removed outlier: 3.913A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.728A 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 274 Processing helix chain 'A' and resid 277 through 280 removed outlier: 3.826A pdb=" N ASN A 280 " --> pdb=" O GLY A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 288 through 306 Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.809A pdb=" N VAL A 339 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 419 Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.686A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 470 through 478 removed outlier: 3.539A pdb=" N VAL A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.615A pdb=" N ARG A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.561A pdb=" N VAL A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.944A pdb=" N ILE A 584 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 4.518A pdb=" N SER A 608 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 3.631A 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 671 removed outlier: 3.593A pdb=" N CYS A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 693 removed outlier: 3.648A pdb=" N SER A 684 " --> pdb=" O PRO A 680 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 712 Proline residue: A 708 - end of helix removed outlier: 3.525A 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: 3.507A pdb=" N VAL A 743 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 747 " --> pdb=" O ALA A 744 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 748 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 752 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 758 " --> pdb=" O ASN A 755 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 761 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 763 " --> pdb=" O ILE A 760 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 764 " --> pdb=" O ARG A 761 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 765 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 767 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 768 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 772 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N CYS A 773 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 776 " --> pdb=" O CYS A 773 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A 777 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 780 " --> pdb=" O THR A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 798 removed outlier: 3.557A pdb=" N ASN A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 806 removed outlier: 4.344A pdb=" N LEU A 806 " --> pdb=" O PRO A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 831 through 856 removed outlier: 3.546A pdb=" N TYR A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 3.670A 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 911 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 950 through 956 removed outlier: 4.631A pdb=" N LEU A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 955 " --> pdb=" O PRO A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 989 Proline residue: A 975 - end of helix removed outlier: 3.730A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1029 removed outlier: 3.529A pdb=" N LEU A1021 " --> pdb=" O PRO A1017 " (cutoff:3.500A) Proline residue: A1024 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 126 through 129 Processing sheet with id= B, first strand: chain 'A' and resid 150 through 153 removed outlier: 6.916A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 331 through 333 removed outlier: 6.657A pdb=" N VAL A 347 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N THR A 700 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS A 349 " --> pdb=" O THR A 700 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG A 619 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER A 350 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.533A 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 378 through 383 removed outlier: 5.242A pdb=" N ASN A 380 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU A 369 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 382 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N PHE A 367 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY A 597 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N MET A 366 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS A 595 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE A 368 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N VAL A 593 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 12.874A pdb=" N ASP A 370 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 16.197A pdb=" N THR A 591 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 483 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.029A 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: 6.905A pdb=" N LEU A 590 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE A 527 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 5.738A 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: 6.429A pdb=" N CYS A 674 " --> pdb=" O PHE A 652 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 174 through 176 removed outlier: 3.538A pdb=" N ALA A 216 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP A 176 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE A 214 " --> pdb=" O ASP A 176 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 3.23 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: 2572 1.35 - 1.48: 1792 1.48 - 1.61: 3523 1.61 - 1.73: 4 1.73 - 1.86: 90 Bond restraints: 7981 Sorted by residual: bond pdb=" C1' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.390 1.616 -0.226 2.00e-02 2.50e+03 1.27e+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 1.299 0.129 2.00e-02 2.50e+03 4.15e+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 3.23e+01 bond pdb=" C2' ACP A2001 " pdb=" O2' ACP A2001 " ideal model delta sigma weight residual 1.401 1.494 -0.093 2.00e-02 2.50e+03 2.15e+01 ... (remaining 7976 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.30: 231 106.30 - 113.23: 4504 113.23 - 120.16: 2682 120.16 - 127.09: 3333 127.09 - 134.02: 89 Bond angle restraints: 10839 Sorted by residual: angle pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O5' ACP A2001 " ideal model delta sigma weight residual 93.75 109.88 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" C3B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O3A ACP A2001 " ideal model delta sigma weight residual 98.05 110.22 -12.17 3.00e+00 1.11e-01 1.64e+01 angle pdb=" N1 ACP A2001 " pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 119.32 108.30 11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O1B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O2B ACP A2001 " ideal model delta sigma weight residual 119.60 108.87 10.73 3.00e+00 1.11e-01 1.28e+01 angle pdb=" O1A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O2A ACP A2001 " ideal model delta sigma weight residual 118.95 109.05 9.90 3.00e+00 1.11e-01 1.09e+01 ... (remaining 10834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.54: 4698 25.54 - 51.08: 144 51.08 - 76.62: 14 76.62 - 102.16: 3 102.16 - 127.70: 1 Dihedral angle restraints: 4860 sinusoidal: 1941 harmonic: 2919 Sorted by residual: 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 78.95 -127.70 1 3.00e+01 1.11e-03 1.72e+01 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 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ASN A 421 " pdb=" C ASN A 421 " pdb=" N ASP A 422 " pdb=" CA ASP A 422 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 4857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1177 0.076 - 0.151: 95 0.151 - 0.227: 0 0.227 - 0.303: 0 0.303 - 0.378: 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 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA PRO A 248 " pdb=" N PRO A 248 " pdb=" C PRO A 248 " pdb=" CB PRO A 248 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA VAL A 194 " pdb=" N VAL A 194 " pdb=" C VAL A 194 " pdb=" CB VAL A 194 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1270 not shown) Planarity restraints: 1376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A1016 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A1017 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1017 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1017 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 502 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO A 503 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " -0.023 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 3.58e-02 2.05e+00 pdb=" N PRO A 975 " 0.062 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 ... (remaining 1373 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 87 2.61 - 3.18: 6702 3.18 - 3.75: 12048 3.75 - 4.33: 17946 4.33 - 4.90: 28887 Nonbonded interactions: 65670 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.035 2.170 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.125 2.170 nonbonded pdb=" O ILE A 307 " pdb=" OE1 GLU A 309 " model vdw 2.137 3.040 nonbonded pdb=" OE2 GLU A 309 " pdb=" OD1 ASN A 795 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASP A 351 " pdb="MG MG A2002 " model vdw 2.191 2.170 ... (remaining 65665 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: 1.470 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.520 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 0.226 7981 Z= 0.360 Angle : 0.642 16.126 10839 Z= 0.341 Chirality : 0.041 0.378 1273 Planarity : 0.004 0.045 1376 Dihedral : 12.490 127.700 2965 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: -3.94 (0.20), residues: 1006 helix: -3.34 (0.14), residues: 484 sheet: -1.64 (0.37), residues: 124 loop : -1.65 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 793 HIS 0.007 0.001 HIS A 566 PHE 0.011 0.001 PHE A 367 TYR 0.006 0.001 TYR A 842 ARG 0.002 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.912 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 1.1038 time to fit residues: 205.3612 Evaluate side-chains 131 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1753 ------------------------------------------------------------------------------- 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: 4.9990 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 19 ASN A 190 HIS A 421 ASN A 453 ASN A 501 ASN A 568 ASN A 582 ASN A 868 GLN A 913 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7981 Z= 0.216 Angle : 0.527 5.565 10839 Z= 0.274 Chirality : 0.043 0.137 1273 Planarity : 0.005 0.049 1376 Dihedral : 8.576 163.644 1102 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.78 % Allowed : 10.53 % Favored : 86.69 % 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: 1006 helix: -0.93 (0.22), residues: 487 sheet: -1.05 (0.42), residues: 119 loop : -0.96 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 854 HIS 0.005 0.001 HIS A 566 PHE 0.013 0.001 PHE A 367 TYR 0.009 0.001 TYR A 842 ARG 0.007 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 0.809 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 142 average time/residue: 1.0367 time to fit residues: 157.3404 Evaluate side-chains 132 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.1319 time to fit residues: 1.7897 ------------------------------------------------------------------------------- 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: 0.0020 chunk 28 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 568 ASN A 582 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7981 Z= 0.137 Angle : 0.464 5.469 10839 Z= 0.240 Chirality : 0.040 0.126 1273 Planarity : 0.004 0.050 1376 Dihedral : 8.424 164.245 1102 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.08 % Allowed : 13.08 % Favored : 84.84 % 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: -0.41 (0.26), residues: 1006 helix: 0.24 (0.24), residues: 487 sheet: -0.76 (0.43), residues: 119 loop : -0.57 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 854 HIS 0.004 0.000 HIS A 566 PHE 0.007 0.001 PHE A 693 TYR 0.010 0.001 TYR A 842 ARG 0.010 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.925 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 133 average time/residue: 1.1694 time to fit residues: 165.7767 Evaluate side-chains 124 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1591 time to fit residues: 1.7549 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 81 optimal weight: 0.4980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN A 453 ASN A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7981 Z= 0.268 Angle : 0.537 5.557 10839 Z= 0.275 Chirality : 0.044 0.138 1273 Planarity : 0.005 0.048 1376 Dihedral : 8.987 179.772 1102 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.78 % Allowed : 14.12 % Favored : 83.10 % 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: -0.30 (0.26), residues: 1006 helix: 0.37 (0.24), residues: 493 sheet: -0.90 (0.43), residues: 122 loop : -0.52 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.006 0.001 HIS A 566 PHE 0.016 0.001 PHE A 367 TYR 0.011 0.002 TYR A 295 ARG 0.009 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 0.898 Fit side-chains outliers start: 24 outliers final: 13 residues processed: 127 average time/residue: 1.1212 time to fit residues: 152.5284 Evaluate side-chains 127 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.3148 time to fit residues: 3.6101 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 40 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 7981 Z= 0.482 Angle : 0.693 8.560 10839 Z= 0.349 Chirality : 0.050 0.196 1273 Planarity : 0.006 0.047 1376 Dihedral : 9.100 157.859 1102 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.36 % Allowed : 14.58 % Favored : 82.06 % 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: -0.72 (0.26), residues: 1006 helix: -0.01 (0.24), residues: 493 sheet: -1.24 (0.43), residues: 110 loop : -0.66 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 107 HIS 0.009 0.001 HIS A 566 PHE 0.025 0.002 PHE A 367 TYR 0.014 0.002 TYR A 295 ARG 0.010 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 0.963 Fit side-chains outliers start: 29 outliers final: 17 residues processed: 131 average time/residue: 1.1350 time to fit residues: 158.6489 Evaluate side-chains 128 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 10 residues processed: 7 average time/residue: 0.2517 time to fit residues: 3.4219 ------------------------------------------------------------------------------- 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: 4.9990 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 582 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7981 Z= 0.169 Angle : 0.499 5.949 10839 Z= 0.256 Chirality : 0.041 0.129 1273 Planarity : 0.004 0.052 1376 Dihedral : 8.840 163.568 1102 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.31 % Allowed : 15.97 % Favored : 81.71 % 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: -0.06 (0.26), residues: 1006 helix: 0.55 (0.24), residues: 492 sheet: -0.82 (0.43), residues: 121 loop : -0.36 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 854 HIS 0.004 0.001 HIS A 566 PHE 0.014 0.001 PHE A 693 TYR 0.009 0.001 TYR A 842 ARG 0.011 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.982 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 126 average time/residue: 1.1439 time to fit residues: 154.2213 Evaluate side-chains 117 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.2307 time to fit residues: 1.5192 ------------------------------------------------------------------------------- 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: 2.9990 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7981 Z= 0.236 Angle : 0.527 5.501 10839 Z= 0.270 Chirality : 0.043 0.136 1273 Planarity : 0.005 0.051 1376 Dihedral : 8.905 163.903 1102 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.78 % Allowed : 16.09 % Favored : 81.13 % 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: 0.01 (0.26), residues: 1006 helix: 0.60 (0.24), residues: 493 sheet: -0.83 (0.45), residues: 106 loop : -0.32 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 854 HIS 0.005 0.001 HIS A 566 PHE 0.016 0.001 PHE A 693 TYR 0.011 0.001 TYR A 842 ARG 0.012 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 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: 24 poor density : 109 time to evaluate : 0.891 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 125 average time/residue: 1.1248 time to fit residues: 150.1912 Evaluate side-chains 121 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.1400 time to fit residues: 1.7489 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.0020 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 93 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7981 Z= 0.142 Angle : 0.476 8.613 10839 Z= 0.243 Chirality : 0.041 0.125 1273 Planarity : 0.004 0.053 1376 Dihedral : 8.707 164.611 1102 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.55 % Allowed : 16.32 % Favored : 81.13 % 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: 0.33 (0.27), residues: 1006 helix: 0.88 (0.25), residues: 489 sheet: -0.58 (0.44), residues: 122 loop : -0.18 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 854 HIS 0.003 0.000 HIS A 566 PHE 0.007 0.001 PHE A 985 TYR 0.010 0.001 TYR A 842 ARG 0.013 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 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 : 0.874 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 121 average time/residue: 1.1343 time to fit residues: 146.7776 Evaluate side-chains 115 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.2194 time to fit residues: 1.4439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.341 > 50: distance: 49 - 53: 34.809 distance: 53 - 54: 50.512 distance: 54 - 55: 64.752 distance: 54 - 57: 51.325 distance: 55 - 56: 53.437 distance: 55 - 58: 57.944 distance: 58 - 59: 48.756 distance: 58 - 64: 54.977 distance: 59 - 60: 67.847 distance: 59 - 62: 57.686 distance: 60 - 61: 69.395 distance: 60 - 65: 40.970 distance: 62 - 63: 39.761 distance: 63 - 64: 49.421 distance: 65 - 66: 56.005 distance: 66 - 67: 56.464 distance: 66 - 69: 57.079 distance: 67 - 68: 55.545 distance: 67 - 73: 57.553 distance: 69 - 70: 41.075 distance: 69 - 71: 20.993 distance: 73 - 74: 36.399 distance: 74 - 75: 37.306 distance: 75 - 77: 65.444 distance: 77 - 78: 60.010 distance: 78 - 79: 23.658 distance: 78 - 81: 48.354 distance: 79 - 80: 57.391 distance: 79 - 86: 55.908 distance: 81 - 82: 38.615 distance: 82 - 83: 64.515 distance: 83 - 84: 36.031 distance: 83 - 85: 42.773 distance: 86 - 87: 11.001 distance: 87 - 88: 15.855 distance: 87 - 90: 37.860 distance: 88 - 89: 22.387 distance: 88 - 93: 35.462 distance: 90 - 91: 7.223 distance: 90 - 92: 45.624 distance: 93 - 94: 67.392 distance: 94 - 95: 62.838 distance: 94 - 97: 38.938 distance: 95 - 96: 41.998 distance: 95 - 103: 63.229 distance: 97 - 98: 57.862 distance: 98 - 99: 68.563 distance: 98 - 100: 56.417 distance: 99 - 101: 41.627 distance: 100 - 102: 70.252 distance: 101 - 102: 64.198 distance: 103 - 104: 20.458 distance: 104 - 105: 36.598 distance: 104 - 107: 23.522 distance: 105 - 106: 50.544 distance: 105 - 112: 38.013 distance: 107 - 108: 46.827 distance: 108 - 109: 45.664 distance: 109 - 110: 11.258 distance: 110 - 111: 42.595 distance: 112 - 113: 42.286 distance: 113 - 116: 57.486 distance: 114 - 115: 54.184 distance: 114 - 120: 28.611 distance: 116 - 117: 41.366 distance: 117 - 118: 27.260 distance: 117 - 119: 55.843 distance: 120 - 121: 33.588 distance: 121 - 122: 43.284 distance: 121 - 124: 34.861 distance: 122 - 123: 26.033 distance: 122 - 128: 21.952 distance: 125 - 126: 4.690