Starting phenix.real_space_refine (version: dev) on Mon Feb 20 05:48:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb1_32392/02_2023/7wb1_32392.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb1_32392/02_2023/7wb1_32392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb1_32392/02_2023/7wb1_32392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb1_32392/02_2023/7wb1_32392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb1_32392/02_2023/7wb1_32392.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb1_32392/02_2023/7wb1_32392.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 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 Process input model Symmetric amino acids flipped Residue "A GLU 76": "OE1" <-> "OE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11524 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 614 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "C" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 547 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2577 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 59, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 106} Chain: "A" Number of atoms: 7786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7786 Classifications: {'peptide': 960} Link IDs: {'PTRANS': 37, 'TRANS': 922} Chain breaks: 2 Time building chain proxies: 6.98, per 1000 atoms: 0.61 Number of scatterers: 11524 At special positions: 0 Unit cell: (101.52, 141, 121.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 178 15.00 O 2598 8.00 N 2059 7.00 C 6661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.33 Conformation dependent library (CDL) restraints added in 1.2 seconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 12 sheets defined 49.4% alpha, 13.1% beta 62 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 60 through 92 removed outlier: 3.735A pdb=" N ARG A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 195 through 201 removed outlier: 3.552A pdb=" N ILE A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 222 through 271 removed outlier: 3.577A pdb=" N ASP A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 309 Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.605A pdb=" N GLU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.748A pdb=" N GLY A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 378 removed outlier: 3.755A pdb=" N GLU A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.807A pdb=" N LYS A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'A' and resid 413 through 443 removed outlier: 4.041A pdb=" N VAL A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR A 418 " --> pdb=" O TRP A 414 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 466 removed outlier: 4.200A pdb=" N LYS A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 472 through 493 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 697 through 717 removed outlier: 3.602A pdb=" N LYS A 701 " --> pdb=" O SER A 697 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 715 " --> pdb=" O VAL A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 725 through 750 Processing helix chain 'A' and resid 770 through 774 Processing helix chain 'A' and resid 776 through 789 Processing helix chain 'A' and resid 793 through 798 removed outlier: 4.163A pdb=" N TYR A 797 " --> pdb=" O PRO A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 829 removed outlier: 3.504A pdb=" N LYS A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 874 Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 886 through 901 removed outlier: 3.754A pdb=" N GLU A 892 " --> pdb=" O GLY A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 937 removed outlier: 3.835A pdb=" N GLN A 924 " --> pdb=" O HIS A 920 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 937 " --> pdb=" O TRP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 949 Processing helix chain 'A' and resid 954 through 971 removed outlier: 3.805A pdb=" N PHE A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 502 through 506 removed outlier: 3.505A pdb=" N SER A 502 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 614 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU A 611 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU A 640 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN A 613 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 36 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 35 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 removed outlier: 4.525A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 135 " --> pdb=" O CYS A 130 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 128 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115 removed outlier: 4.525A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 155 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 145 removed outlier: 3.629A pdb=" N GLN A 144 " --> pdb=" O HIS A 152 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 152 " --> pdb=" O GLN A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 542 through 545 removed outlier: 3.504A pdb=" N ARG A 542 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 573 " --> pdb=" O ARG A 542 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 572 " --> pdb=" O PHE A 556 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A 556 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL A 559 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N PHE A 517 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N ASN A 561 " --> pdb=" O CYS A 515 " (cutoff:3.500A) removed outlier: 12.651A pdb=" N CYS A 515 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 622 through 623 Processing sheet with id=AA8, first strand: chain 'A' and resid 691 through 694 removed outlier: 4.777A pdb=" N ALA A 756 " --> pdb=" O ILE A 658 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR A 801 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE A 755 " --> pdb=" O THR A 801 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 682 Processing sheet with id=AB1, first strand: chain 'A' and resid 830 through 831 removed outlier: 3.513A pdb=" N LYS A 830 " --> pdb=" O MET A 837 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 850 through 853 removed outlier: 4.192A pdb=" N TYR A 853 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL A 862 " --> pdb=" O TYR A 853 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 910 through 911 382 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 150 hydrogen bonds 276 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2385 1.33 - 1.45: 3515 1.45 - 1.57: 5830 1.57 - 1.69: 353 1.69 - 1.81: 41 Bond restraints: 12124 Sorted by residual: bond pdb=" CG LEU A 70 " pdb=" CD2 LEU A 70 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.69e+00 bond pdb=" N1 C D 103 " pdb=" C2 C D 103 " ideal model delta sigma weight residual 1.397 1.422 -0.025 2.00e-02 2.50e+03 1.59e+00 bond pdb=" C2 C D 104 " pdb=" O2 C D 104 " ideal model delta sigma weight residual 1.240 1.216 0.024 2.00e-02 2.50e+03 1.50e+00 bond pdb=" O4' DG B 19 " pdb=" C1' DG B 19 " ideal model delta sigma weight residual 1.414 1.395 0.019 2.00e-02 2.50e+03 9.34e-01 bond pdb=" CG ARG A 967 " pdb=" CD ARG A 967 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.98e-01 ... (remaining 12119 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.74: 1004 105.74 - 112.81: 6650 112.81 - 119.88: 4154 119.88 - 126.94: 4849 126.94 - 134.01: 514 Bond angle restraints: 17171 Sorted by residual: angle pdb=" N TYR A 854 " pdb=" CA TYR A 854 " pdb=" C TYR A 854 " ideal model delta sigma weight residual 107.32 112.15 -4.83 1.65e+00 3.67e-01 8.57e+00 angle pdb=" C GLU A 439 " pdb=" N GLU A 440 " pdb=" CA GLU A 440 " ideal model delta sigma weight residual 121.94 116.41 5.53 2.00e+00 2.50e-01 7.63e+00 angle pdb=" C2' G D 73 " pdb=" C1' G D 73 " pdb=" N9 G D 73 " ideal model delta sigma weight residual 112.00 115.74 -3.74 1.50e+00 4.44e-01 6.23e+00 angle pdb=" C TYR A 966 " pdb=" N ARG A 967 " pdb=" CA ARG A 967 " ideal model delta sigma weight residual 121.14 116.80 4.34 1.75e+00 3.27e-01 6.14e+00 angle pdb=" O3' G D 45 " pdb=" C3' G D 45 " pdb=" C2' G D 45 " ideal model delta sigma weight residual 113.70 117.36 -3.66 1.50e+00 4.44e-01 5.95e+00 ... (remaining 17166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 6488 35.91 - 71.82: 364 71.82 - 107.73: 27 107.73 - 143.64: 3 143.64 - 179.55: 6 Dihedral angle restraints: 6888 sinusoidal: 4086 harmonic: 2802 Sorted by residual: dihedral pdb=" O4' U D 11 " pdb=" C1' U D 11 " pdb=" N1 U D 11 " pdb=" C2 U D 11 " ideal model delta sinusoidal sigma weight residual -128.00 51.55 -179.55 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U D 17 " pdb=" C1' U D 17 " pdb=" N1 U D 17 " pdb=" C2 U D 17 " ideal model delta sinusoidal sigma weight residual -128.00 50.22 -178.22 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U D 9 " pdb=" C1' U D 9 " pdb=" N1 U D 9 " pdb=" C2 U D 9 " ideal model delta sinusoidal sigma weight residual -160.00 -100.01 -59.99 1 1.50e+01 4.44e-03 2.13e+01 ... (remaining 6885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1634 0.045 - 0.089: 268 0.089 - 0.134: 68 0.134 - 0.178: 8 0.178 - 0.223: 1 Chirality restraints: 1979 Sorted by residual: chirality pdb=" C1' G D 73 " pdb=" O4' G D 73 " pdb=" C2' G D 73 " pdb=" N9 G D 73 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C3' C D 41 " pdb=" C4' C D 41 " pdb=" O3' C D 41 " pdb=" C2' C D 41 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" C3' G D 45 " pdb=" C4' G D 45 " pdb=" O3' G D 45 " pdb=" C2' G D 45 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.17 2.00e-01 2.50e+01 7.50e-01 ... (remaining 1976 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C D 104 " 0.009 2.00e-02 2.50e+03 2.56e-02 1.47e+01 pdb=" N1 C D 104 " -0.006 2.00e-02 2.50e+03 pdb=" C2 C D 104 " -0.063 2.00e-02 2.50e+03 pdb=" O2 C D 104 " 0.039 2.00e-02 2.50e+03 pdb=" N3 C D 104 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C D 104 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C D 104 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C D 104 " 0.010 2.00e-02 2.50e+03 pdb=" C6 C D 104 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C D 118 " 0.022 2.00e-02 2.50e+03 1.66e-02 6.17e+00 pdb=" N1 C D 118 " -0.033 2.00e-02 2.50e+03 pdb=" C2 C D 118 " 0.007 2.00e-02 2.50e+03 pdb=" O2 C D 118 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C D 118 " -0.000 2.00e-02 2.50e+03 pdb=" C4 C D 118 " 0.025 2.00e-02 2.50e+03 pdb=" N4 C D 118 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C D 118 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C D 118 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 56 " -0.006 2.00e-02 2.50e+03 1.42e-02 5.57e+00 pdb=" N9 A D 56 " -0.000 2.00e-02 2.50e+03 pdb=" C8 A D 56 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A D 56 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A D 56 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A D 56 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A D 56 " 0.000 2.00e-02 2.50e+03 pdb=" N1 A D 56 " -0.033 2.00e-02 2.50e+03 pdb=" C2 A D 56 " 0.031 2.00e-02 2.50e+03 pdb=" N3 A D 56 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A D 56 " -0.002 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 183 2.62 - 3.19: 9664 3.19 - 3.76: 19864 3.76 - 4.33: 25399 4.33 - 4.90: 38127 Nonbonded interactions: 93237 Sorted by model distance: nonbonded pdb=" N2 G D 59 " pdb=" O2 C D 94 " model vdw 2.046 2.496 nonbonded pdb=" OP2 G D 101 " pdb=" NH2 ARG A 591 " model vdw 2.182 2.520 nonbonded pdb=" NZ LYS A 521 " pdb=" OE2 GLU A 605 " model vdw 2.227 2.520 nonbonded pdb=" O6 DG B 22 " pdb=" NZ LYS A 227 " model vdw 2.236 2.520 nonbonded pdb=" OG1 THR A 202 " pdb=" OE1 GLU A 204 " model vdw 2.263 2.440 ... (remaining 93232 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 178 5.49 5 S 28 5.16 5 C 6661 2.51 5 N 2059 2.21 5 O 2598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.730 Check model and map are aligned: 0.180 Process input model: 37.870 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 12124 Z= 0.170 Angle : 0.590 6.604 17171 Z= 0.317 Chirality : 0.037 0.223 1979 Planarity : 0.004 0.044 1546 Dihedral : 19.513 179.554 5078 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.18 % Rotamer Outliers : 0.00 % 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: 0.55 (0.28), residues: 954 helix: 1.86 (0.26), residues: 412 sheet: -0.69 (0.45), residues: 140 loop : -0.80 (0.31), residues: 402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2350 time to fit residues: 29.2896 Evaluate side-chains 57 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 53 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS A 729 ASN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 12124 Z= 0.163 Angle : 0.582 7.246 17171 Z= 0.310 Chirality : 0.037 0.216 1979 Planarity : 0.004 0.045 1546 Dihedral : 21.496 179.093 3068 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.60 % Rotamer Outliers : 1.19 % 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: 0.66 (0.28), residues: 954 helix: 1.94 (0.26), residues: 426 sheet: -0.72 (0.44), residues: 140 loop : -0.79 (0.32), residues: 388 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 1.128 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 68 average time/residue: 0.2091 time to fit residues: 22.6425 Evaluate side-chains 63 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1663 time to fit residues: 2.9600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 101 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 82 optimal weight: 7.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 12124 Z= 0.164 Angle : 0.557 7.831 17171 Z= 0.296 Chirality : 0.036 0.178 1979 Planarity : 0.004 0.046 1546 Dihedral : 21.395 178.729 3068 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.83 % 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 (0.28), residues: 954 helix: 1.97 (0.26), residues: 427 sheet: -0.58 (0.46), residues: 135 loop : -0.79 (0.31), residues: 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 1.195 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 0.2112 time to fit residues: 22.7328 Evaluate side-chains 62 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1004 time to fit residues: 2.3112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 0.0060 chunk 69 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 12124 Z= 0.130 Angle : 0.523 9.505 17171 Z= 0.277 Chirality : 0.035 0.176 1979 Planarity : 0.004 0.048 1546 Dihedral : 21.288 178.250 3068 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 1.07 % 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: 0.99 (0.29), residues: 954 helix: 2.16 (0.26), residues: 427 sheet: -0.36 (0.47), residues: 134 loop : -0.64 (0.32), residues: 393 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 1.078 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 75 average time/residue: 0.2048 time to fit residues: 24.3001 Evaluate side-chains 62 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1231 time to fit residues: 1.6087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 27 optimal weight: 0.0470 chunk 36 optimal weight: 3.9990 overall best weight: 2.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS A 284 GLN A 520 GLN A 729 ASN A 804 GLN A 945 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 12124 Z= 0.211 Angle : 0.580 7.120 17171 Z= 0.308 Chirality : 0.037 0.193 1979 Planarity : 0.004 0.048 1546 Dihedral : 21.442 179.067 3068 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 1.55 % 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: 0.71 (0.28), residues: 954 helix: 1.96 (0.26), residues: 426 sheet: -0.81 (0.44), residues: 149 loop : -0.68 (0.32), residues: 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 70 average time/residue: 0.2090 time to fit residues: 23.3414 Evaluate side-chains 69 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1591 time to fit residues: 4.0007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 12124 Z= 0.244 Angle : 0.618 8.247 17171 Z= 0.326 Chirality : 0.038 0.185 1979 Planarity : 0.004 0.049 1546 Dihedral : 21.514 179.016 3068 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.95 % 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: 0.28 (0.28), residues: 954 helix: 1.57 (0.25), residues: 426 sheet: -1.05 (0.44), residues: 149 loop : -0.85 (0.32), residues: 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 1.095 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 68 average time/residue: 0.1891 time to fit residues: 21.5019 Evaluate side-chains 59 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1251 time to fit residues: 2.0612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 30.0000 chunk 62 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 12124 Z= 0.147 Angle : 0.554 8.250 17171 Z= 0.292 Chirality : 0.036 0.180 1979 Planarity : 0.004 0.054 1546 Dihedral : 21.394 178.792 3068 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.29), residues: 954 helix: 1.96 (0.26), residues: 426 sheet: -0.91 (0.44), residues: 150 loop : -0.71 (0.33), residues: 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 1.133 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 68 average time/residue: 0.2114 time to fit residues: 23.1437 Evaluate side-chains 61 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1141 time to fit residues: 2.2330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 10 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 12124 Z= 0.151 Angle : 0.560 8.858 17171 Z= 0.293 Chirality : 0.036 0.179 1979 Planarity : 0.004 0.054 1546 Dihedral : 21.382 179.162 3068 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.29), residues: 954 helix: 1.96 (0.26), residues: 426 sheet: -0.86 (0.45), residues: 150 loop : -0.69 (0.33), residues: 378 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 1.156 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 0.1978 time to fit residues: 20.2788 Evaluate side-chains 59 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1251 time to fit residues: 2.2548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.2980 chunk 104 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 306 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 : 0.004 0.044 12124 Z= 0.261 Angle : 0.656 9.653 17171 Z= 0.341 Chirality : 0.039 0.187 1979 Planarity : 0.004 0.050 1546 Dihedral : 21.569 179.680 3068 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 0.24 % 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: 0.17 (0.28), residues: 954 helix: 1.49 (0.25), residues: 424 sheet: -1.14 (0.44), residues: 150 loop : -0.88 (0.32), residues: 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 1.070 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.2081 time to fit residues: 21.1755 Evaluate side-chains 53 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1136 time to fit residues: 1.6159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 27 optimal weight: 0.2980 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 12124 Z= 0.213 Angle : 0.615 9.775 17171 Z= 0.322 Chirality : 0.038 0.185 1979 Planarity : 0.004 0.051 1546 Dihedral : 21.482 179.034 3068 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 0.36 % 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: 0.18 (0.28), residues: 954 helix: 1.49 (0.25), residues: 425 sheet: -1.11 (0.43), residues: 160 loop : -0.86 (0.33), residues: 369 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 1.325 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.2384 time to fit residues: 23.6880 Evaluate side-chains 57 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1102 time to fit residues: 1.7804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.093877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.068170 restraints weight = 43577.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.070252 restraints weight = 23597.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.071562 restraints weight = 16605.871| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 12124 Z= 0.175 Angle : 0.587 9.497 17171 Z= 0.308 Chirality : 0.037 0.183 1979 Planarity : 0.004 0.055 1546 Dihedral : 21.425 178.860 3068 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.00 % 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 (0.28), residues: 954 helix: 1.63 (0.26), residues: 425 sheet: -1.04 (0.45), residues: 150 loop : -0.83 (0.33), residues: 379 =============================================================================== Job complete usr+sys time: 1833.37 seconds wall clock time: 35 minutes 2.53 seconds (2102.53 seconds total)