Starting phenix.real_space_refine on Thu Feb 15 07:11:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb1_32392/02_2024/7wb1_32392.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb1_32392/02_2024/7wb1_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_2024/7wb1_32392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb1_32392/02_2024/7wb1_32392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb1_32392/02_2024/7wb1_32392.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb1_32392/02_2024/7wb1_32392.pdb" } resolution = 3.7 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= 0.002 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 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. 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.70, per 1000 atoms: 0.58 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: 6.58 Conformation dependent library (CDL) restraints added in 1.5 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: 4.74 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: 5.97 Time building geometry restraints manager: 6.88 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: 6686 35.91 - 71.82: 558 71.82 - 107.73: 49 107.73 - 143.64: 3 143.64 - 179.55: 6 Dihedral angle restraints: 7302 sinusoidal: 4500 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 7299 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 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: 0.590 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: 3.410 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 40.700 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 22.125 179.554 5492 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 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 962 HIS 0.015 0.002 HIS A 435 PHE 0.016 0.001 PHE A 332 TYR 0.017 0.001 TYR A 857 ARG 0.003 0.000 ARG A 764 *********************** 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 : 1.029 Fit side-chains REVERT: A 29 MET cc_start: 0.6906 (ppp) cc_final: 0.5886 (ppp) REVERT: A 375 GLN cc_start: 0.7736 (mm110) cc_final: 0.7534 (tp40) REVERT: A 570 MET cc_start: 0.7668 (tpt) cc_final: 0.7458 (mmm) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2326 time to fit residues: 28.8268 Evaluate side-chains 58 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12124 Z= 0.157 Angle : 0.569 6.662 17171 Z= 0.302 Chirality : 0.037 0.192 1979 Planarity : 0.004 0.046 1546 Dihedral : 24.754 178.870 3482 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 0.95 % Allowed : 7.51 % Favored : 91.54 % 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: -0.57 (0.45), residues: 136 loop : -0.80 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 366 HIS 0.005 0.001 HIS A 435 PHE 0.025 0.001 PHE A 399 TYR 0.011 0.001 TYR A 857 ARG 0.002 0.000 ARG A 764 *********************** 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 75 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.6887 (ppp) cc_final: 0.5921 (ppp) outliers start: 8 outliers final: 5 residues processed: 70 average time/residue: 0.2004 time to fit residues: 22.1953 Evaluate side-chains 64 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 961 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS A 160 ASN A 284 GLN A 375 GLN A 520 GLN A 654 ASN A 804 GLN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12124 Z= 0.346 Angle : 0.736 12.206 17171 Z= 0.385 Chirality : 0.043 0.193 1979 Planarity : 0.005 0.049 1546 Dihedral : 24.911 179.109 3482 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.15 % Allowed : 11.32 % Favored : 86.53 % 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: -0.23 (0.27), residues: 954 helix: 1.14 (0.24), residues: 424 sheet: -1.20 (0.45), residues: 133 loop : -1.16 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 782 HIS 0.008 0.002 HIS A 435 PHE 0.021 0.002 PHE A 399 TYR 0.019 0.002 TYR A 857 ARG 0.005 0.001 ARG A 642 *********************** 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 73 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 55 time to evaluate : 1.137 Fit side-chains REVERT: A 134 CYS cc_start: 0.8102 (m) cc_final: 0.7516 (t) REVERT: A 486 TRP cc_start: 0.6952 (m-10) cc_final: 0.6665 (m-10) outliers start: 18 outliers final: 13 residues processed: 64 average time/residue: 0.1909 time to fit residues: 20.5065 Evaluate side-chains 61 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 961 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 0.0970 chunk 103 optimal weight: 20.0000 chunk 109 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7545 moved from start: 0.1807 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= 0.145 Angle : 0.566 9.080 17171 Z= 0.299 Chirality : 0.036 0.181 1979 Planarity : 0.004 0.048 1546 Dihedral : 24.662 179.833 3482 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.31 % Allowed : 12.63 % Favored : 86.05 % 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: 0.49 (0.28), residues: 954 helix: 1.78 (0.26), residues: 426 sheet: -0.85 (0.45), residues: 140 loop : -0.84 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 598 HIS 0.014 0.001 HIS A 152 PHE 0.013 0.001 PHE A 399 TYR 0.011 0.001 TYR A 744 ARG 0.002 0.000 ARG A 967 *********************** 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 80 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 1.257 Fit side-chains REVERT: A 29 MET cc_start: 0.6538 (ppp) cc_final: 0.5944 (ppp) REVERT: A 134 CYS cc_start: 0.7992 (m) cc_final: 0.7382 (t) REVERT: A 231 ASP cc_start: 0.8610 (p0) cc_final: 0.8282 (p0) REVERT: A 486 TRP cc_start: 0.6875 (m-10) cc_final: 0.6586 (m-10) REVERT: A 489 ASP cc_start: 0.7579 (m-30) cc_final: 0.7340 (m-30) outliers start: 11 outliers final: 5 residues processed: 77 average time/residue: 0.2078 time to fit residues: 24.9380 Evaluate side-chains 67 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 732 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 81 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 30.0000 chunk 27 optimal weight: 0.0770 chunk 36 optimal weight: 6.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 945 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12124 Z= 0.147 Angle : 0.545 8.014 17171 Z= 0.291 Chirality : 0.036 0.177 1979 Planarity : 0.004 0.049 1546 Dihedral : 24.600 179.407 3482 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.91 % Allowed : 13.35 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.28), residues: 954 helix: 1.93 (0.26), residues: 426 sheet: -0.57 (0.47), residues: 135 loop : -0.81 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 782 HIS 0.004 0.001 HIS A 435 PHE 0.032 0.001 PHE A 399 TYR 0.008 0.001 TYR A 418 ARG 0.002 0.000 ARG A 778 *********************** 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 79 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.6596 (ppp) cc_final: 0.5975 (ppp) REVERT: A 134 CYS cc_start: 0.7978 (m) cc_final: 0.7361 (t) REVERT: A 489 ASP cc_start: 0.7574 (m-30) cc_final: 0.7355 (m-30) REVERT: A 710 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7801 (mt-10) outliers start: 16 outliers final: 11 residues processed: 73 average time/residue: 0.1840 time to fit residues: 22.1338 Evaluate side-chains 68 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 961 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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: 0.7597 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12124 Z= 0.231 Angle : 0.615 8.241 17171 Z= 0.325 Chirality : 0.038 0.242 1979 Planarity : 0.004 0.049 1546 Dihedral : 24.710 179.792 3482 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.38 % Allowed : 13.95 % Favored : 83.67 % 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 (0.25), residues: 424 sheet: -0.79 (0.46), residues: 133 loop : -0.96 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 782 HIS 0.005 0.001 HIS A 251 PHE 0.014 0.002 PHE A 463 TYR 0.015 0.002 TYR A 138 ARG 0.004 0.001 ARG A 443 *********************** 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 80 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 134 CYS cc_start: 0.7998 (m) cc_final: 0.7470 (t) REVERT: A 710 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7830 (mt-10) REVERT: A 857 TYR cc_start: -0.0371 (OUTLIER) cc_final: -0.1461 (t80) outliers start: 20 outliers final: 15 residues processed: 73 average time/residue: 0.2160 time to fit residues: 24.7675 Evaluate side-chains 69 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 857 TYR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 967 ARG 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: 5.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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: 0.7535 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12124 Z= 0.139 Angle : 0.551 8.618 17171 Z= 0.290 Chirality : 0.036 0.181 1979 Planarity : 0.004 0.054 1546 Dihedral : 24.616 178.825 3482 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.79 % Allowed : 15.14 % Favored : 83.08 % 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 (0.28), residues: 954 helix: 1.95 (0.26), residues: 426 sheet: -0.85 (0.41), residues: 160 loop : -0.72 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 598 HIS 0.003 0.001 HIS A 405 PHE 0.011 0.001 PHE A 463 TYR 0.008 0.001 TYR A 85 ARG 0.004 0.000 ARG A 478 *********************** 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 77 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 CYS cc_start: 0.7954 (m) cc_final: 0.7424 (t) REVERT: A 341 GLU cc_start: 0.6550 (mm-30) cc_final: 0.6316 (tp30) REVERT: A 489 ASP cc_start: 0.7547 (m-30) cc_final: 0.7312 (m-30) REVERT: A 710 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7751 (mt-10) REVERT: A 837 MET cc_start: 0.4859 (mmt) cc_final: 0.3598 (ppp) REVERT: A 857 TYR cc_start: -0.0453 (OUTLIER) cc_final: -0.1475 (t80) outliers start: 15 outliers final: 9 residues processed: 74 average time/residue: 0.1968 time to fit residues: 23.2484 Evaluate side-chains 70 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 857 TYR Chi-restraints excluded: chain A residue 967 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.7549 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12124 Z= 0.157 Angle : 0.556 8.990 17171 Z= 0.292 Chirality : 0.036 0.176 1979 Planarity : 0.004 0.053 1546 Dihedral : 24.618 179.410 3482 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.15 % Allowed : 14.90 % Favored : 82.96 % 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 (0.29), residues: 954 helix: 1.93 (0.26), residues: 426 sheet: -0.81 (0.42), residues: 160 loop : -0.71 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 782 HIS 0.002 0.001 HIS A 251 PHE 0.034 0.001 PHE A 399 TYR 0.008 0.001 TYR A 698 ARG 0.002 0.000 ARG A 778 *********************** 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 78 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 CYS cc_start: 0.7977 (m) cc_final: 0.7443 (t) REVERT: A 489 ASP cc_start: 0.7634 (m-30) cc_final: 0.7347 (m-30) REVERT: A 710 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7765 (mt-10) REVERT: A 837 MET cc_start: 0.4890 (mmt) cc_final: 0.3628 (ppp) REVERT: A 857 TYR cc_start: -0.0380 (OUTLIER) cc_final: -0.1431 (t80) outliers start: 18 outliers final: 13 residues processed: 72 average time/residue: 0.2026 time to fit residues: 23.0348 Evaluate side-chains 72 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 857 TYR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 967 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 44 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 91 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.7551 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12124 Z= 0.157 Angle : 0.559 11.105 17171 Z= 0.294 Chirality : 0.036 0.177 1979 Planarity : 0.004 0.053 1546 Dihedral : 24.624 179.425 3482 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.91 % Allowed : 15.38 % Favored : 82.72 % 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: 0.68 (0.29), residues: 954 helix: 1.94 (0.26), residues: 425 sheet: -0.80 (0.42), residues: 160 loop : -0.68 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 782 HIS 0.003 0.001 HIS A 251 PHE 0.037 0.001 PHE A 399 TYR 0.008 0.001 TYR A 138 ARG 0.002 0.000 ARG A 774 *********************** 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 79 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 CYS cc_start: 0.7978 (m) cc_final: 0.7447 (t) REVERT: A 489 ASP cc_start: 0.7568 (m-30) cc_final: 0.7355 (m-30) REVERT: A 710 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7813 (mt-10) REVERT: A 837 MET cc_start: 0.4894 (mmt) cc_final: 0.3631 (ppp) REVERT: A 857 TYR cc_start: -0.0391 (OUTLIER) cc_final: -0.1442 (t80) outliers start: 16 outliers final: 14 residues processed: 74 average time/residue: 0.2108 time to fit residues: 24.3536 Evaluate side-chains 75 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 857 TYR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 967 ARG 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: 1.9990 chunk 112 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 27 optimal weight: 0.0040 overall best weight: 1.3798 ------------------------------------------------------------------------------- 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: 0.7547 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12124 Z= 0.155 Angle : 0.557 9.230 17171 Z= 0.293 Chirality : 0.036 0.176 1979 Planarity : 0.004 0.053 1546 Dihedral : 24.623 179.248 3482 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.67 % Allowed : 15.73 % Favored : 82.60 % 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: 1.89 (0.26), residues: 425 sheet: -0.74 (0.43), residues: 160 loop : -0.67 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 486 HIS 0.003 0.001 HIS A 251 PHE 0.038 0.001 PHE A 399 TYR 0.008 0.001 TYR A 138 ARG 0.006 0.000 ARG A 774 ********************** 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 76 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 CYS cc_start: 0.7960 (m) cc_final: 0.7427 (t) REVERT: A 489 ASP cc_start: 0.7565 (m-30) cc_final: 0.7336 (m-30) REVERT: A 710 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7800 (mt-10) REVERT: A 837 MET cc_start: 0.4963 (mmt) cc_final: 0.3650 (ppp) REVERT: A 857 TYR cc_start: -0.0443 (OUTLIER) cc_final: -0.1464 (t80) outliers start: 14 outliers final: 13 residues processed: 72 average time/residue: 0.2052 time to fit residues: 23.2979 Evaluate side-chains 75 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 857 TYR Chi-restraints excluded: chain A residue 967 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.094136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.068551 restraints weight = 43851.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.070634 restraints weight = 23658.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.071945 restraints weight = 16671.966| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2483 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= 0.159 Angle : 0.565 9.248 17171 Z= 0.297 Chirality : 0.036 0.176 1979 Planarity : 0.004 0.053 1546 Dihedral : 24.618 179.247 3482 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.79 % Allowed : 15.85 % Favored : 82.36 % 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: 0.67 (0.29), residues: 954 helix: 1.90 (0.26), residues: 425 sheet: -0.73 (0.43), residues: 160 loop : -0.68 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 782 HIS 0.003 0.001 HIS A 251 PHE 0.037 0.001 PHE A 399 TYR 0.008 0.001 TYR A 719 ARG 0.002 0.000 ARG A 778 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1942.71 seconds wall clock time: 36 minutes 46.83 seconds (2206.83 seconds total)