Starting phenix.real_space_refine on Thu Sep 26 07:11:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7by0_30239/09_2024/7by0_30239.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7by0_30239/09_2024/7by0_30239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7by0_30239/09_2024/7by0_30239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7by0_30239/09_2024/7by0_30239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7by0_30239/09_2024/7by0_30239.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7by0_30239/09_2024/7by0_30239.cif" } resolution = 4.5 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= 0.001 sd= 0.004 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 288 5.49 5 S 12 5.16 5 C 7083 2.51 5 N 2407 2.21 5 O 2903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12693 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 854 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "B" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 854 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "F" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2914 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2949 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "K" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 363 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TPO:plan-1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "L" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 366 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TPO:plan-1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 7.63, per 1000 atoms: 0.60 Number of scatterers: 12693 At special positions: 0 Unit cell: (86.9, 123.2, 115.5, 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 12 16.00 P 288 15.00 O 2903 8.00 N 2407 7.00 C 7083 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1628 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 65.6% alpha, 1.2% beta 140 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 6.12 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.595A pdb=" N PHE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N CYS A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 117 removed outlier: 3.582A pdb=" N ALA A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.766A pdb=" N LEU A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.042A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.828A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.624A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 71 removed outlier: 4.491A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.827A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 47 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.611A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.870A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.543A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 75 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 117 removed outlier: 3.558A pdb=" N LEU E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 133 removed outlier: 3.641A pdb=" N LEU E 127 " --> pdb=" O TYR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 138 removed outlier: 4.000A pdb=" N GLN E 137 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY E 138 " --> pdb=" O GLY E 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 134 through 138' Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.680A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.953A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.514A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.402A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.955A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.606A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.724A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 629 through 640 removed outlier: 3.964A pdb=" N LYS K 633 " --> pdb=" O HIS K 629 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU K 636 " --> pdb=" O ILE K 632 " (cutoff:3.500A) Processing helix chain 'L' and resid 629 through 640 removed outlier: 4.107A pdb=" N LYS L 633 " --> pdb=" O HIS L 629 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 97 removed outlier: 7.069A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.390A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'E' and resid 86 through 87 removed outlier: 7.150A pdb=" N ARG E 86 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.433A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 385 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 720 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 5.43 Time building geometry restraints manager: 3.71 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: 2364 1.33 - 1.45: 4427 1.45 - 1.57: 6115 1.57 - 1.69: 576 1.69 - 1.81: 20 Bond restraints: 13502 Sorted by residual: bond pdb=" OG1 TPO K 651 " pdb=" P TPO K 651 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" OG1 TPO L 651 " pdb=" P TPO L 651 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C1' DA J 165 " pdb=" N9 DA J 165 " ideal model delta sigma weight residual 1.460 1.370 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" O3P TPO K 651 " pdb=" P TPO K 651 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O3P TPO L 651 " pdb=" P TPO L 651 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 13497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 18820 2.36 - 4.73: 608 4.73 - 7.09: 33 7.09 - 9.45: 10 9.45 - 11.81: 2 Bond angle restraints: 19473 Sorted by residual: angle pdb=" CB TPO L 651 " pdb=" OG1 TPO L 651 " pdb=" P TPO L 651 " ideal model delta sigma weight residual 119.31 107.50 11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CB TPO K 651 " pdb=" OG1 TPO K 651 " pdb=" P TPO K 651 " ideal model delta sigma weight residual 119.31 107.64 11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C3' DT J 285 " pdb=" C2' DT J 285 " pdb=" C1' DT J 285 " ideal model delta sigma weight residual 101.60 95.99 5.61 1.50e+00 4.44e-01 1.40e+01 angle pdb=" C3' DG I 100 " pdb=" C2' DG I 100 " pdb=" C1' DG I 100 " ideal model delta sigma weight residual 101.60 96.61 4.99 1.50e+00 4.44e-01 1.11e+01 angle pdb=" C3' DA I 68 " pdb=" C2' DA I 68 " pdb=" C1' DA I 68 " ideal model delta sigma weight residual 101.60 96.64 4.96 1.50e+00 4.44e-01 1.09e+01 ... (remaining 19468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 4790 22.35 - 44.69: 1469 44.69 - 67.04: 1002 67.04 - 89.39: 115 89.39 - 111.74: 8 Dihedral angle restraints: 7384 sinusoidal: 4864 harmonic: 2520 Sorted by residual: dihedral pdb=" CA ARG E 41 " pdb=" C ARG E 41 " pdb=" N TYR E 42 " pdb=" CA TYR E 42 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA LEU K 662 " pdb=" C LEU K 662 " pdb=" N LYS K 663 " pdb=" CA LYS K 663 " ideal model delta harmonic sigma weight residual 180.00 158.86 21.14 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 7381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1676 0.058 - 0.115: 442 0.115 - 0.173: 85 0.173 - 0.231: 9 0.231 - 0.289: 1 Chirality restraints: 2213 Sorted by residual: chirality pdb=" CB ILE B 29 " pdb=" CA ILE B 29 " pdb=" CG1 ILE B 29 " pdb=" CG2 ILE B 29 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA LYS F 31 " pdb=" N LYS F 31 " pdb=" C LYS F 31 " pdb=" CB LYS F 31 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB ILE L 660 " pdb=" CA ILE L 660 " pdb=" CG1 ILE L 660 " pdb=" CG2 ILE L 660 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2210 not shown) Planarity restraints: 1473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 120 " 0.035 2.00e-02 2.50e+03 1.55e-02 7.24e+00 pdb=" N9 DG I 120 " -0.035 2.00e-02 2.50e+03 pdb=" C8 DG I 120 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 120 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 120 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DG I 120 " 0.007 2.00e-02 2.50e+03 pdb=" O6 DG I 120 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DG I 120 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 120 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 120 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 120 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 120 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 18 " -0.036 2.00e-02 2.50e+03 1.54e-02 7.14e+00 pdb=" N9 DG I 18 " 0.030 2.00e-02 2.50e+03 pdb=" C8 DG I 18 " 0.012 2.00e-02 2.50e+03 pdb=" N7 DG I 18 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 18 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DG I 18 " -0.015 2.00e-02 2.50e+03 pdb=" O6 DG I 18 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 18 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG I 18 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 18 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DG I 18 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 18 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 665 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C LEU K 665 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU K 665 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU K 666 " -0.015 2.00e-02 2.50e+03 ... (remaining 1470 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 140 2.54 - 3.13: 9094 3.13 - 3.72: 26032 3.72 - 4.31: 32371 4.31 - 4.90: 45647 Nonbonded interactions: 113284 Sorted by model distance: nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG K 659 " model vdw 1.950 3.120 nonbonded pdb=" OE2 GLU G 92 " pdb=" NH1 ARG L 659 " model vdw 2.048 3.120 nonbonded pdb=" OE1 GLU D 105 " pdb=" N ILE K 660 " model vdw 2.206 3.120 nonbonded pdb=" OG SER G 40 " pdb=" O SER H 87 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR E 80 " pdb=" O VAL E 83 " model vdw 2.254 3.040 ... (remaining 113279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 11 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 31 through 107 or (resid 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 109 through 124)) } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 628 through 644 or (resid 645 and (name N or name CA or na \ me C or name O or name CB )) or resid 646 through 679)) } 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: 0.500 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.710 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 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 : 0.008 0.111 13502 Z= 0.405 Angle : 0.966 11.815 19473 Z= 0.564 Chirality : 0.054 0.289 2213 Planarity : 0.007 0.060 1473 Dihedral : 31.228 111.735 5756 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.15 % Allowed : 11.39 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.22), residues: 838 helix: -2.11 (0.16), residues: 532 sheet: None (None), residues: 0 loop : -2.64 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP L 668 HIS 0.008 0.002 HIS F 75 PHE 0.015 0.003 PHE E 79 TYR 0.014 0.002 TYR F 98 ARG 0.008 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.9464 (m-10) cc_final: 0.9137 (m-10) REVERT: A 66 GLN cc_start: 0.9711 (mm-40) cc_final: 0.9316 (mp10) REVERT: A 74 GLU cc_start: 0.8962 (tt0) cc_final: 0.8322 (mt-10) REVERT: A 85 TYR cc_start: 0.9499 (m-80) cc_final: 0.9244 (m-80) REVERT: A 128 GLN cc_start: 0.9521 (mt0) cc_final: 0.9296 (mm-40) REVERT: A 131 ARG cc_start: 0.9357 (ttt-90) cc_final: 0.9132 (ptm160) REVERT: B 60 VAL cc_start: 0.9565 (m) cc_final: 0.9215 (p) REVERT: B 63 GLU cc_start: 0.9469 (mt-10) cc_final: 0.9160 (mt-10) REVERT: B 74 GLU cc_start: 0.9478 (tm-30) cc_final: 0.9217 (tm-30) REVERT: B 84 MET cc_start: 0.9404 (mmm) cc_final: 0.8993 (mmm) REVERT: C 36 LYS cc_start: 0.9453 (mtpt) cc_final: 0.9019 (mmtp) REVERT: C 61 GLU cc_start: 0.9089 (tp30) cc_final: 0.8831 (mm-30) REVERT: C 75 LYS cc_start: 0.9786 (mmtt) cc_final: 0.9492 (mmtm) REVERT: C 87 ILE cc_start: 0.9864 (mm) cc_final: 0.9465 (tp) REVERT: C 95 LYS cc_start: 0.9820 (ttmt) cc_final: 0.9505 (tptp) REVERT: D 80 LEU cc_start: 0.9736 (tp) cc_final: 0.9531 (tt) REVERT: D 99 ARG cc_start: 0.9422 (mtt180) cc_final: 0.8804 (ttm110) REVERT: E 55 TYR cc_start: 0.9609 (m-10) cc_final: 0.9363 (m-10) REVERT: E 85 TYR cc_start: 0.9350 (m-10) cc_final: 0.9131 (m-80) REVERT: E 90 MET cc_start: 0.9315 (tmm) cc_final: 0.9049 (tmm) REVERT: E 95 LEU cc_start: 0.9883 (tp) cc_final: 0.9677 (pp) REVERT: E 100 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9298 (mt-10) REVERT: E 128 GLN cc_start: 0.9605 (tt0) cc_final: 0.9153 (mm-40) REVERT: F 31 LYS cc_start: 0.9743 (pptt) cc_final: 0.9509 (ptmm) REVERT: F 60 VAL cc_start: 0.9472 (m) cc_final: 0.8946 (p) REVERT: F 63 GLU cc_start: 0.9402 (mt-10) cc_final: 0.9077 (mt-10) REVERT: F 74 GLU cc_start: 0.9548 (tt0) cc_final: 0.9147 (tm-30) REVERT: F 79 LYS cc_start: 0.9670 (mmtm) cc_final: 0.8926 (ttpp) REVERT: G 95 LYS cc_start: 0.9794 (tttm) cc_final: 0.9578 (tptm) REVERT: H 68 ASP cc_start: 0.9233 (t70) cc_final: 0.8912 (t0) REVERT: H 71 GLU cc_start: 0.9234 (pp20) cc_final: 0.9025 (pp20) REVERT: H 72 ARG cc_start: 0.9554 (ttm170) cc_final: 0.9307 (ptm160) REVERT: H 80 LEU cc_start: 0.9463 (tp) cc_final: 0.9089 (tp) REVERT: H 99 ARG cc_start: 0.9499 (mtt90) cc_final: 0.8717 (ttm110) REVERT: L 665 LEU cc_start: 0.9255 (tt) cc_final: 0.9040 (tp) outliers start: 1 outliers final: 1 residues processed: 213 average time/residue: 0.3514 time to fit residues: 99.3858 Evaluate side-chains 141 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 GLN A 88 GLN A 96 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 104 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 95 GLN E 96 GLN ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 112 GLN H 49 HIS K 650 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13502 Z= 0.316 Angle : 0.730 8.404 19473 Z= 0.434 Chirality : 0.042 0.224 2213 Planarity : 0.006 0.048 1473 Dihedral : 35.042 128.426 4104 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.15 % Allowed : 4.67 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.27), residues: 838 helix: -0.02 (0.20), residues: 546 sheet: None (None), residues: 0 loop : -2.38 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 668 HIS 0.006 0.002 HIS B 75 PHE 0.013 0.002 PHE E 68 TYR 0.025 0.002 TYR F 72 ARG 0.004 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.9504 (m-10) cc_final: 0.9047 (m-10) REVERT: A 66 GLN cc_start: 0.9713 (mm110) cc_final: 0.9324 (mp10) REVERT: A 68 PHE cc_start: 0.9528 (t80) cc_final: 0.8976 (t80) REVERT: A 74 GLU cc_start: 0.9121 (tt0) cc_final: 0.8499 (mt-10) REVERT: A 85 TYR cc_start: 0.9578 (m-80) cc_final: 0.9112 (m-80) REVERT: A 96 GLN cc_start: 0.9165 (tp-100) cc_final: 0.8655 (tp40) REVERT: A 97 GLU cc_start: 0.9505 (mt-10) cc_final: 0.8939 (mt-10) REVERT: A 100 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8989 (mt-10) REVERT: B 53 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8613 (tm-30) REVERT: B 59 LYS cc_start: 0.9691 (ptmt) cc_final: 0.9443 (ptmm) REVERT: B 63 GLU cc_start: 0.9427 (mt-10) cc_final: 0.9013 (mt-10) REVERT: B 84 MET cc_start: 0.9379 (mmm) cc_final: 0.9129 (mmt) REVERT: C 36 LYS cc_start: 0.9508 (mtpt) cc_final: 0.9078 (mmtp) REVERT: C 87 ILE cc_start: 0.9781 (mm) cc_final: 0.9429 (tp) REVERT: D 72 ARG cc_start: 0.9553 (ttm170) cc_final: 0.9323 (ptm160) REVERT: D 95 GLN cc_start: 0.9733 (tt0) cc_final: 0.8764 (tm-30) REVERT: D 99 ARG cc_start: 0.9407 (mtt180) cc_final: 0.8807 (tpp80) REVERT: D 113 GLU cc_start: 0.9659 (mm-30) cc_final: 0.9377 (mt-10) REVERT: E 68 PHE cc_start: 0.9577 (t80) cc_final: 0.9368 (t80) REVERT: E 90 MET cc_start: 0.9225 (tmm) cc_final: 0.8963 (tmm) REVERT: E 95 LEU cc_start: 0.9895 (tp) cc_final: 0.9688 (pp) REVERT: E 96 GLN cc_start: 0.9125 (tp-100) cc_final: 0.8902 (tp40) REVERT: E 97 GLU cc_start: 0.9416 (tt0) cc_final: 0.8783 (tt0) REVERT: E 100 GLU cc_start: 0.9458 (mt-10) cc_final: 0.9182 (mt-10) REVERT: E 128 GLN cc_start: 0.9681 (OUTLIER) cc_final: 0.9293 (mm110) REVERT: E 139 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8861 (mp0) REVERT: F 49 LEU cc_start: 0.9629 (mp) cc_final: 0.9204 (mp) REVERT: F 60 VAL cc_start: 0.9591 (m) cc_final: 0.9149 (p) REVERT: F 63 GLU cc_start: 0.9404 (mt-10) cc_final: 0.9187 (mp0) REVERT: F 74 GLU cc_start: 0.9594 (tt0) cc_final: 0.9194 (tm-30) REVERT: F 79 LYS cc_start: 0.9643 (mptt) cc_final: 0.9093 (ttpp) REVERT: G 73 ASN cc_start: 0.9336 (t0) cc_final: 0.9021 (m110) REVERT: G 87 ILE cc_start: 0.9867 (mm) cc_final: 0.9527 (tp) REVERT: G 91 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8858 (mm-30) REVERT: G 111 ILE cc_start: 0.9493 (tp) cc_final: 0.9260 (tp) REVERT: H 59 MET cc_start: 0.8845 (tpt) cc_final: 0.8520 (tpp) REVERT: H 72 ARG cc_start: 0.9621 (ttm170) cc_final: 0.9312 (ptm160) REVERT: H 80 LEU cc_start: 0.9664 (tp) cc_final: 0.9322 (tp) REVERT: H 99 ARG cc_start: 0.9579 (mtt90) cc_final: 0.8858 (ttm110) REVERT: H 113 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8465 (tm-30) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.2456 time to fit residues: 63.4232 Evaluate side-chains 143 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13502 Z= 0.331 Angle : 0.720 8.874 19473 Z= 0.430 Chirality : 0.041 0.176 2213 Planarity : 0.006 0.052 1473 Dihedral : 35.030 132.379 4104 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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: -0.46 (0.28), residues: 838 helix: 0.68 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -2.22 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 87 HIS 0.011 0.002 HIS B 75 PHE 0.009 0.002 PHE D 65 TYR 0.016 0.002 TYR C 57 ARG 0.008 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.9693 (mm110) cc_final: 0.9327 (mp10) REVERT: A 68 PHE cc_start: 0.9552 (t80) cc_final: 0.9195 (t80) REVERT: A 74 GLU cc_start: 0.9107 (tt0) cc_final: 0.8528 (mt-10) REVERT: A 85 TYR cc_start: 0.9566 (m-80) cc_final: 0.9119 (m-80) REVERT: A 96 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8660 (tp40) REVERT: A 97 GLU cc_start: 0.9500 (mt-10) cc_final: 0.8914 (mt-10) REVERT: A 100 GLU cc_start: 0.9263 (mt-10) cc_final: 0.9027 (mt-10) REVERT: B 53 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8623 (tm-30) REVERT: B 59 LYS cc_start: 0.9716 (ptmt) cc_final: 0.9343 (ptmm) REVERT: B 63 GLU cc_start: 0.9453 (mt-10) cc_final: 0.8966 (mp0) REVERT: B 84 MET cc_start: 0.9441 (mmm) cc_final: 0.9017 (mmm) REVERT: C 36 LYS cc_start: 0.9536 (mtpt) cc_final: 0.9061 (mmtp) REVERT: C 87 ILE cc_start: 0.9794 (mm) cc_final: 0.9432 (tp) REVERT: D 68 ASP cc_start: 0.9243 (t70) cc_final: 0.8605 (t0) REVERT: D 72 ARG cc_start: 0.9615 (ttm170) cc_final: 0.8903 (ptm160) REVERT: D 95 GLN cc_start: 0.9730 (tt0) cc_final: 0.9050 (tt0) REVERT: D 99 ARG cc_start: 0.9396 (mtt180) cc_final: 0.8769 (ttm110) REVERT: E 51 GLU cc_start: 0.9677 (mm-30) cc_final: 0.9401 (mm-30) REVERT: E 68 PHE cc_start: 0.9572 (t80) cc_final: 0.8920 (t80) REVERT: E 74 GLU cc_start: 0.9443 (mt-10) cc_final: 0.9134 (mt-10) REVERT: E 90 MET cc_start: 0.9239 (tmm) cc_final: 0.8932 (tmm) REVERT: E 96 GLN cc_start: 0.9028 (tp-100) cc_final: 0.8796 (tp40) REVERT: E 97 GLU cc_start: 0.9475 (tt0) cc_final: 0.8886 (tt0) REVERT: E 128 GLN cc_start: 0.9707 (tt0) cc_final: 0.9267 (tp40) REVERT: E 139 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8847 (mp0) REVERT: F 74 GLU cc_start: 0.9578 (tt0) cc_final: 0.9154 (tm-30) REVERT: F 79 LYS cc_start: 0.9660 (mptt) cc_final: 0.9156 (ttpp) REVERT: G 73 ASN cc_start: 0.9389 (t0) cc_final: 0.9094 (m110) REVERT: G 91 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8844 (mm-30) REVERT: G 95 LYS cc_start: 0.9688 (tttp) cc_final: 0.9339 (tptm) REVERT: H 59 MET cc_start: 0.8890 (tpt) cc_final: 0.8634 (tpp) REVERT: H 80 LEU cc_start: 0.9689 (tp) cc_final: 0.9394 (tp) REVERT: H 99 ARG cc_start: 0.9596 (mtt90) cc_final: 0.8840 (ttm110) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3081 time to fit residues: 74.6980 Evaluate side-chains 132 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13502 Z= 0.282 Angle : 0.692 12.928 19473 Z= 0.410 Chirality : 0.041 0.172 2213 Planarity : 0.005 0.044 1473 Dihedral : 34.962 131.986 4104 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.15 % Allowed : 4.67 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.28), residues: 838 helix: 0.88 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -2.09 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 87 HIS 0.011 0.002 HIS B 75 PHE 0.011 0.002 PHE E 102 TYR 0.017 0.002 TYR C 57 ARG 0.015 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TYR cc_start: 0.9616 (m-80) cc_final: 0.9120 (m-80) REVERT: A 96 GLN cc_start: 0.9024 (tp-100) cc_final: 0.8762 (tp40) REVERT: A 97 GLU cc_start: 0.9508 (mt-10) cc_final: 0.8997 (mt-10) REVERT: B 53 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8518 (tm-30) REVERT: B 59 LYS cc_start: 0.9744 (ptmt) cc_final: 0.9407 (ptmm) REVERT: B 60 VAL cc_start: 0.9590 (m) cc_final: 0.9152 (p) REVERT: B 63 GLU cc_start: 0.9446 (mt-10) cc_final: 0.8983 (mp0) REVERT: B 72 TYR cc_start: 0.9719 (m-80) cc_final: 0.9384 (m-10) REVERT: B 84 MET cc_start: 0.9410 (mmm) cc_final: 0.9051 (mmm) REVERT: C 36 LYS cc_start: 0.9514 (mtpt) cc_final: 0.9039 (mmtp) REVERT: C 87 ILE cc_start: 0.9805 (mm) cc_final: 0.9443 (tp) REVERT: C 102 ILE cc_start: 0.9400 (tp) cc_final: 0.9196 (tp) REVERT: D 72 ARG cc_start: 0.9592 (ttm170) cc_final: 0.9387 (ptm160) REVERT: D 95 GLN cc_start: 0.9648 (tt0) cc_final: 0.9106 (tt0) REVERT: D 99 ARG cc_start: 0.9383 (mtt180) cc_final: 0.8749 (ttm110) REVERT: E 51 GLU cc_start: 0.9675 (mm-30) cc_final: 0.9397 (mm-30) REVERT: E 74 GLU cc_start: 0.9405 (mt-10) cc_final: 0.9051 (mt-10) REVERT: E 85 TYR cc_start: 0.9525 (m-10) cc_final: 0.8971 (m-80) REVERT: E 90 MET cc_start: 0.9294 (tmm) cc_final: 0.9028 (tmm) REVERT: E 96 GLN cc_start: 0.9333 (tp-100) cc_final: 0.8889 (tm-30) REVERT: E 97 GLU cc_start: 0.9231 (tt0) cc_final: 0.8837 (tt0) REVERT: E 128 GLN cc_start: 0.9710 (tt0) cc_final: 0.9183 (tp-100) REVERT: E 139 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8731 (mp0) REVERT: F 62 LEU cc_start: 0.9857 (mm) cc_final: 0.9609 (mm) REVERT: F 63 GLU cc_start: 0.9364 (mt-10) cc_final: 0.8975 (mm-30) REVERT: F 74 GLU cc_start: 0.9551 (tt0) cc_final: 0.9057 (tm-30) REVERT: F 79 LYS cc_start: 0.9641 (mptt) cc_final: 0.9209 (ttpp) REVERT: G 73 ASN cc_start: 0.9396 (t0) cc_final: 0.9130 (m110) REVERT: G 95 LYS cc_start: 0.9678 (tttp) cc_final: 0.9349 (tptm) REVERT: H 59 MET cc_start: 0.8877 (tpt) cc_final: 0.8674 (tpp) REVERT: H 80 LEU cc_start: 0.9694 (tp) cc_final: 0.9420 (tp) REVERT: H 99 ARG cc_start: 0.9597 (mtt90) cc_final: 0.8806 (ttm110) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.2940 time to fit residues: 73.5182 Evaluate side-chains 139 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 0.0370 chunk 95 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 overall best weight: 6.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13502 Z= 0.323 Angle : 0.708 13.148 19473 Z= 0.418 Chirality : 0.041 0.168 2213 Planarity : 0.005 0.044 1473 Dihedral : 35.023 132.736 4104 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: -0.05 (0.28), residues: 838 helix: 0.95 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.96 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 87 HIS 0.010 0.002 HIS B 75 PHE 0.012 0.002 PHE C 25 TYR 0.019 0.002 TYR C 57 ARG 0.010 0.001 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.9499 (t80) cc_final: 0.9126 (t80) REVERT: A 74 GLU cc_start: 0.9141 (tt0) cc_final: 0.8694 (mt-10) REVERT: A 85 TYR cc_start: 0.9614 (m-80) cc_final: 0.9157 (m-80) REVERT: A 96 GLN cc_start: 0.9241 (tp-100) cc_final: 0.8860 (tp40) REVERT: A 97 GLU cc_start: 0.9484 (mt-10) cc_final: 0.9064 (mt-10) REVERT: B 59 LYS cc_start: 0.9746 (ptmt) cc_final: 0.9408 (ptmm) REVERT: B 63 GLU cc_start: 0.9468 (mt-10) cc_final: 0.8958 (mp0) REVERT: B 72 TYR cc_start: 0.9706 (m-80) cc_final: 0.9408 (m-80) REVERT: C 36 LYS cc_start: 0.9540 (mtpt) cc_final: 0.9052 (mmtp) REVERT: C 95 LYS cc_start: 0.9703 (tptm) cc_final: 0.9388 (tptp) REVERT: C 102 ILE cc_start: 0.9430 (tp) cc_final: 0.9064 (tp) REVERT: D 95 GLN cc_start: 0.9709 (tt0) cc_final: 0.9013 (tt0) REVERT: D 99 ARG cc_start: 0.9394 (mtt180) cc_final: 0.8738 (ttm110) REVERT: E 51 GLU cc_start: 0.9650 (mm-30) cc_final: 0.9409 (mm-30) REVERT: E 74 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9086 (mt-10) REVERT: E 85 TYR cc_start: 0.9574 (m-10) cc_final: 0.8991 (m-80) REVERT: E 90 MET cc_start: 0.9288 (tmm) cc_final: 0.9012 (tmm) REVERT: E 96 GLN cc_start: 0.9316 (tp-100) cc_final: 0.8807 (tm-30) REVERT: E 97 GLU cc_start: 0.9332 (tt0) cc_final: 0.8862 (tt0) REVERT: E 128 GLN cc_start: 0.9726 (tt0) cc_final: 0.9165 (tp-100) REVERT: F 74 GLU cc_start: 0.9574 (tt0) cc_final: 0.9152 (tm-30) REVERT: F 79 LYS cc_start: 0.9657 (mptt) cc_final: 0.9190 (ttpp) REVERT: G 73 ASN cc_start: 0.9413 (t0) cc_final: 0.9129 (m110) REVERT: G 95 LYS cc_start: 0.9673 (tttp) cc_final: 0.9360 (tptm) REVERT: G 102 ILE cc_start: 0.9348 (mm) cc_final: 0.9080 (mt) REVERT: H 59 MET cc_start: 0.8799 (tpt) cc_final: 0.8526 (tpp) REVERT: H 80 LEU cc_start: 0.9672 (tp) cc_final: 0.9424 (tp) REVERT: H 99 ARG cc_start: 0.9587 (mtt90) cc_final: 0.8845 (ttm110) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3054 time to fit residues: 74.9063 Evaluate side-chains 132 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13502 Z= 0.257 Angle : 0.678 12.956 19473 Z= 0.399 Chirality : 0.040 0.157 2213 Planarity : 0.005 0.044 1473 Dihedral : 34.944 132.245 4104 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: 0.07 (0.29), residues: 838 helix: 1.04 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.88 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 87 HIS 0.009 0.001 HIS B 75 PHE 0.012 0.002 PHE E 79 TYR 0.024 0.002 TYR F 51 ARG 0.008 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.9454 (t80) cc_final: 0.8931 (t80) REVERT: A 74 GLU cc_start: 0.9344 (tt0) cc_final: 0.8646 (mt-10) REVERT: A 85 TYR cc_start: 0.9590 (m-80) cc_final: 0.9078 (m-80) REVERT: A 97 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9100 (mt-10) REVERT: A 137 GLN cc_start: 0.9166 (mp10) cc_final: 0.8703 (mp10) REVERT: B 59 LYS cc_start: 0.9736 (ptmt) cc_final: 0.9390 (ptmm) REVERT: B 60 VAL cc_start: 0.9583 (m) cc_final: 0.9161 (p) REVERT: B 63 GLU cc_start: 0.9455 (mt-10) cc_final: 0.8987 (mp0) REVERT: B 72 TYR cc_start: 0.9703 (m-80) cc_final: 0.9394 (m-80) REVERT: C 36 LYS cc_start: 0.9555 (mtpt) cc_final: 0.9072 (mmtp) REVERT: C 102 ILE cc_start: 0.9411 (tp) cc_final: 0.8931 (tp) REVERT: D 34 LYS cc_start: 0.8265 (mppt) cc_final: 0.8056 (mmtm) REVERT: D 57 LYS cc_start: 0.9527 (mmmt) cc_final: 0.9228 (mmmt) REVERT: D 68 ASP cc_start: 0.9327 (t70) cc_final: 0.8766 (t0) REVERT: D 71 GLU cc_start: 0.9235 (pp20) cc_final: 0.8835 (pp20) REVERT: D 72 ARG cc_start: 0.9591 (ttm170) cc_final: 0.8913 (ptm160) REVERT: D 95 GLN cc_start: 0.9703 (tt0) cc_final: 0.8964 (tt0) REVERT: D 99 ARG cc_start: 0.9353 (mtt180) cc_final: 0.8737 (ttm110) REVERT: E 51 GLU cc_start: 0.9661 (mm-30) cc_final: 0.9407 (mm-30) REVERT: E 60 GLU cc_start: 0.9522 (pm20) cc_final: 0.9316 (pm20) REVERT: E 68 PHE cc_start: 0.9464 (t80) cc_final: 0.9262 (t80) REVERT: E 85 TYR cc_start: 0.9560 (m-10) cc_final: 0.9001 (m-80) REVERT: E 90 MET cc_start: 0.9263 (tmm) cc_final: 0.9001 (tmm) REVERT: E 96 GLN cc_start: 0.9410 (tp-100) cc_final: 0.8969 (tp40) REVERT: E 109 ASP cc_start: 0.9094 (m-30) cc_final: 0.8678 (m-30) REVERT: E 128 GLN cc_start: 0.9738 (tt0) cc_final: 0.9225 (tp-100) REVERT: E 139 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8684 (mp0) REVERT: F 74 GLU cc_start: 0.9556 (tt0) cc_final: 0.9110 (tm-30) REVERT: F 79 LYS cc_start: 0.9665 (mptt) cc_final: 0.9207 (ttpp) REVERT: G 73 ASN cc_start: 0.9380 (t0) cc_final: 0.9112 (m110) REVERT: G 95 LYS cc_start: 0.9668 (tttp) cc_final: 0.9331 (tptm) REVERT: H 59 MET cc_start: 0.8919 (tpt) cc_final: 0.8632 (tpp) REVERT: H 80 LEU cc_start: 0.9681 (tp) cc_final: 0.9443 (tp) REVERT: H 99 ARG cc_start: 0.9584 (mtt90) cc_final: 0.8795 (ttm110) REVERT: H 113 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8628 (tm-30) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2981 time to fit residues: 75.0867 Evaluate side-chains 137 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13502 Z= 0.251 Angle : 0.671 13.175 19473 Z= 0.395 Chirality : 0.040 0.151 2213 Planarity : 0.005 0.044 1473 Dihedral : 34.824 132.358 4104 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 838 helix: 1.11 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.74 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 87 HIS 0.009 0.001 HIS B 75 PHE 0.015 0.002 PHE A 68 TYR 0.023 0.001 TYR C 57 ARG 0.012 0.000 ARG L 656 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.9282 (tt0) cc_final: 0.8599 (mt-10) REVERT: A 85 TYR cc_start: 0.9586 (m-80) cc_final: 0.9061 (m-80) REVERT: A 97 GLU cc_start: 0.9464 (mt-10) cc_final: 0.8841 (tp30) REVERT: A 100 GLU cc_start: 0.9432 (mt-10) cc_final: 0.9193 (mt-10) REVERT: A 104 VAL cc_start: 0.9537 (m) cc_final: 0.9213 (p) REVERT: A 108 GLU cc_start: 0.9544 (pm20) cc_final: 0.9328 (pm20) REVERT: B 59 LYS cc_start: 0.9715 (ptmt) cc_final: 0.9366 (ptmm) REVERT: B 60 VAL cc_start: 0.9589 (m) cc_final: 0.9136 (p) REVERT: B 63 GLU cc_start: 0.9448 (mt-10) cc_final: 0.8982 (mp0) REVERT: B 72 TYR cc_start: 0.9700 (m-80) cc_final: 0.9383 (m-10) REVERT: B 84 MET cc_start: 0.9483 (mmp) cc_final: 0.9181 (mmp) REVERT: C 36 LYS cc_start: 0.9548 (mtpt) cc_final: 0.9074 (mmtp) REVERT: D 57 LYS cc_start: 0.9508 (mmmt) cc_final: 0.9198 (mmmt) REVERT: D 72 ARG cc_start: 0.9582 (ttm170) cc_final: 0.9368 (ptm160) REVERT: D 95 GLN cc_start: 0.9685 (tt0) cc_final: 0.8933 (tt0) REVERT: D 99 ARG cc_start: 0.9337 (mtt180) cc_final: 0.8720 (ttm110) REVERT: E 51 GLU cc_start: 0.9670 (mm-30) cc_final: 0.9384 (mm-30) REVERT: E 85 TYR cc_start: 0.9571 (m-10) cc_final: 0.8983 (m-80) REVERT: E 90 MET cc_start: 0.9285 (tmm) cc_final: 0.8999 (tmm) REVERT: E 97 GLU cc_start: 0.9654 (tt0) cc_final: 0.9268 (tt0) REVERT: E 104 VAL cc_start: 0.9576 (m) cc_final: 0.9268 (p) REVERT: E 108 GLU cc_start: 0.9520 (pm20) cc_final: 0.9247 (pm20) REVERT: E 128 GLN cc_start: 0.9735 (tt0) cc_final: 0.9228 (tp-100) REVERT: E 139 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8642 (mp0) REVERT: F 66 ILE cc_start: 0.9891 (mt) cc_final: 0.9612 (tt) REVERT: F 74 GLU cc_start: 0.9564 (tt0) cc_final: 0.9127 (tm-30) REVERT: F 79 LYS cc_start: 0.9669 (mptt) cc_final: 0.9205 (ttpp) REVERT: G 73 ASN cc_start: 0.9369 (t0) cc_final: 0.9081 (m110) REVERT: G 95 LYS cc_start: 0.9648 (tttp) cc_final: 0.9337 (tptt) REVERT: H 59 MET cc_start: 0.8920 (tpt) cc_final: 0.8622 (tpp) REVERT: H 80 LEU cc_start: 0.9687 (tp) cc_final: 0.9461 (tp) REVERT: H 99 ARG cc_start: 0.9591 (mtt90) cc_final: 0.8780 (ttm110) REVERT: H 113 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8642 (tm-30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.3001 time to fit residues: 74.3736 Evaluate side-chains 135 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13502 Z= 0.260 Angle : 0.674 13.704 19473 Z= 0.395 Chirality : 0.040 0.163 2213 Planarity : 0.005 0.044 1473 Dihedral : 34.769 132.622 4104 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: 0.29 (0.29), residues: 838 helix: 1.09 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.53 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 87 HIS 0.009 0.001 HIS B 75 PHE 0.022 0.002 PHE A 68 TYR 0.026 0.001 TYR C 57 ARG 0.011 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.9295 (tt0) cc_final: 0.8618 (mt-10) REVERT: A 85 TYR cc_start: 0.9594 (m-80) cc_final: 0.9042 (m-80) REVERT: A 97 GLU cc_start: 0.9473 (mt-10) cc_final: 0.8828 (tp30) REVERT: A 100 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9229 (mt-10) REVERT: B 59 LYS cc_start: 0.9712 (ptmt) cc_final: 0.9372 (ptmm) REVERT: B 60 VAL cc_start: 0.9587 (m) cc_final: 0.9131 (p) REVERT: B 63 GLU cc_start: 0.9452 (mt-10) cc_final: 0.8984 (mp0) REVERT: B 72 TYR cc_start: 0.9697 (m-80) cc_final: 0.9388 (m-80) REVERT: B 87 VAL cc_start: 0.9814 (t) cc_final: 0.9597 (t) REVERT: B 91 LYS cc_start: 0.9403 (ttpp) cc_final: 0.8908 (pttm) REVERT: C 36 LYS cc_start: 0.9545 (mtpt) cc_final: 0.9122 (mmtp) REVERT: D 57 LYS cc_start: 0.9530 (mmmt) cc_final: 0.9253 (mmmt) REVERT: D 72 ARG cc_start: 0.9592 (ttm170) cc_final: 0.9365 (ptm160) REVERT: D 95 GLN cc_start: 0.9684 (tt0) cc_final: 0.8935 (tt0) REVERT: D 99 ARG cc_start: 0.9331 (mtt180) cc_final: 0.8724 (ttm110) REVERT: E 51 GLU cc_start: 0.9658 (mm-30) cc_final: 0.9374 (mm-30) REVERT: E 60 GLU cc_start: 0.9477 (pm20) cc_final: 0.9276 (pm20) REVERT: E 85 TYR cc_start: 0.9559 (m-10) cc_final: 0.8977 (m-80) REVERT: E 97 GLU cc_start: 0.9686 (tt0) cc_final: 0.9303 (tt0) REVERT: E 128 GLN cc_start: 0.9735 (tt0) cc_final: 0.9233 (tp-100) REVERT: E 139 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8641 (mp0) REVERT: F 66 ILE cc_start: 0.9878 (mt) cc_final: 0.9614 (tt) REVERT: F 74 GLU cc_start: 0.9567 (tt0) cc_final: 0.9140 (tm-30) REVERT: F 79 LYS cc_start: 0.9658 (mptt) cc_final: 0.9180 (ttpp) REVERT: G 73 ASN cc_start: 0.9354 (t0) cc_final: 0.9060 (m110) REVERT: G 95 LYS cc_start: 0.9651 (tttp) cc_final: 0.9344 (tptt) REVERT: H 59 MET cc_start: 0.8917 (tpt) cc_final: 0.8565 (tpp) REVERT: H 72 ARG cc_start: 0.9743 (ttm170) cc_final: 0.9506 (ptm160) REVERT: H 80 LEU cc_start: 0.9725 (tp) cc_final: 0.9492 (tp) REVERT: H 99 ARG cc_start: 0.9575 (mtt90) cc_final: 0.8762 (ttm110) REVERT: H 113 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8654 (tm-30) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2942 time to fit residues: 70.8112 Evaluate side-chains 137 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 101 optimal weight: 0.0670 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 overall best weight: 3.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13502 Z= 0.222 Angle : 0.655 12.576 19473 Z= 0.383 Chirality : 0.039 0.157 2213 Planarity : 0.005 0.044 1473 Dihedral : 34.625 132.680 4104 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.29), residues: 838 helix: 1.16 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.37 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 87 HIS 0.008 0.001 HIS B 75 PHE 0.015 0.002 PHE A 102 TYR 0.026 0.001 TYR C 57 ARG 0.009 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.9316 (tt0) cc_final: 0.8584 (mt-10) REVERT: A 85 TYR cc_start: 0.9585 (m-80) cc_final: 0.9025 (m-80) REVERT: A 97 GLU cc_start: 0.9486 (mt-10) cc_final: 0.8794 (tp30) REVERT: A 100 GLU cc_start: 0.9446 (mt-10) cc_final: 0.9225 (mt-10) REVERT: A 137 GLN cc_start: 0.9023 (mp10) cc_final: 0.8638 (mp10) REVERT: B 59 LYS cc_start: 0.9712 (ptmt) cc_final: 0.9369 (ptmm) REVERT: B 60 VAL cc_start: 0.9577 (m) cc_final: 0.9112 (p) REVERT: B 63 GLU cc_start: 0.9441 (mt-10) cc_final: 0.8982 (mp0) REVERT: B 72 TYR cc_start: 0.9700 (m-80) cc_final: 0.9392 (m-80) REVERT: B 87 VAL cc_start: 0.9807 (t) cc_final: 0.9597 (t) REVERT: B 91 LYS cc_start: 0.9421 (ttpp) cc_final: 0.8893 (pttm) REVERT: C 36 LYS cc_start: 0.9544 (mtpt) cc_final: 0.9092 (mmtp) REVERT: D 57 LYS cc_start: 0.9504 (mmmt) cc_final: 0.9122 (mmmt) REVERT: D 59 MET cc_start: 0.9207 (tpt) cc_final: 0.8986 (tpp) REVERT: D 99 ARG cc_start: 0.9315 (mtt180) cc_final: 0.8723 (ttm110) REVERT: E 85 TYR cc_start: 0.9550 (m-10) cc_final: 0.8975 (m-80) REVERT: E 97 GLU cc_start: 0.9683 (tt0) cc_final: 0.9252 (tt0) REVERT: E 128 GLN cc_start: 0.9749 (tt0) cc_final: 0.9267 (tp-100) REVERT: E 139 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8638 (mp0) REVERT: F 66 ILE cc_start: 0.9879 (mt) cc_final: 0.9590 (tt) REVERT: F 74 GLU cc_start: 0.9558 (tt0) cc_final: 0.9127 (tm-30) REVERT: F 79 LYS cc_start: 0.9653 (mptt) cc_final: 0.9152 (ttpp) REVERT: G 95 LYS cc_start: 0.9649 (tttp) cc_final: 0.9340 (tptt) REVERT: H 59 MET cc_start: 0.8913 (tpt) cc_final: 0.8591 (tpp) REVERT: H 72 ARG cc_start: 0.9709 (ttm170) cc_final: 0.9470 (ptm160) REVERT: H 79 ARG cc_start: 0.9440 (ptp90) cc_final: 0.9215 (ptp90) REVERT: H 80 LEU cc_start: 0.9712 (tp) cc_final: 0.9472 (tp) REVERT: H 99 ARG cc_start: 0.9563 (mtt90) cc_final: 0.8725 (ttm110) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2867 time to fit residues: 68.8215 Evaluate side-chains 134 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13502 Z= 0.321 Angle : 0.701 14.715 19473 Z= 0.410 Chirality : 0.040 0.168 2213 Planarity : 0.006 0.072 1473 Dihedral : 34.726 133.783 4104 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.29), residues: 838 helix: 1.03 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.39 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 87 HIS 0.010 0.001 HIS B 75 PHE 0.017 0.002 PHE A 102 TYR 0.026 0.002 TYR C 57 ARG 0.009 0.001 ARG D 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.9298 (tt0) cc_final: 0.8622 (mt-10) REVERT: A 85 TYR cc_start: 0.9602 (m-80) cc_final: 0.9079 (m-80) REVERT: A 97 GLU cc_start: 0.9496 (mt-10) cc_final: 0.8831 (pt0) REVERT: A 100 GLU cc_start: 0.9490 (mt-10) cc_final: 0.9278 (mt-10) REVERT: B 49 LEU cc_start: 0.9818 (mp) cc_final: 0.9511 (mp) REVERT: B 59 LYS cc_start: 0.9729 (ptmt) cc_final: 0.9393 (ptmm) REVERT: B 60 VAL cc_start: 0.9601 (m) cc_final: 0.9169 (p) REVERT: B 63 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9005 (mp0) REVERT: B 72 TYR cc_start: 0.9688 (m-80) cc_final: 0.9430 (m-80) REVERT: B 87 VAL cc_start: 0.9818 (t) cc_final: 0.9592 (t) REVERT: B 91 LYS cc_start: 0.9445 (ttpp) cc_final: 0.8937 (pttm) REVERT: C 36 LYS cc_start: 0.9555 (mtpt) cc_final: 0.9022 (mmtp) REVERT: D 57 LYS cc_start: 0.9581 (mmmt) cc_final: 0.9205 (mmmt) REVERT: D 59 MET cc_start: 0.9184 (tpt) cc_final: 0.8821 (tpp) REVERT: D 68 ASP cc_start: 0.9338 (t70) cc_final: 0.9033 (t0) REVERT: D 71 GLU cc_start: 0.9126 (pp20) cc_final: 0.8847 (pp20) REVERT: D 95 GLN cc_start: 0.9705 (tt0) cc_final: 0.8968 (tt0) REVERT: D 99 ARG cc_start: 0.9348 (mtt180) cc_final: 0.8737 (ttm110) REVERT: E 51 GLU cc_start: 0.9657 (mm-30) cc_final: 0.9401 (mm-30) REVERT: E 85 TYR cc_start: 0.9570 (m-10) cc_final: 0.9053 (m-80) REVERT: E 90 MET cc_start: 0.9120 (tmm) cc_final: 0.8908 (tmm) REVERT: E 97 GLU cc_start: 0.9670 (tt0) cc_final: 0.9239 (tt0) REVERT: E 102 PHE cc_start: 0.9594 (t80) cc_final: 0.9199 (t80) REVERT: E 108 GLU cc_start: 0.9456 (pm20) cc_final: 0.9253 (pm20) REVERT: E 128 GLN cc_start: 0.9725 (tt0) cc_final: 0.9201 (tp-100) REVERT: F 66 ILE cc_start: 0.9878 (mt) cc_final: 0.9597 (tt) REVERT: F 74 GLU cc_start: 0.9577 (tt0) cc_final: 0.9160 (tm-30) REVERT: F 79 LYS cc_start: 0.9641 (mptt) cc_final: 0.9114 (ttpp) REVERT: G 95 LYS cc_start: 0.9665 (tttp) cc_final: 0.9398 (tptt) REVERT: H 59 MET cc_start: 0.8889 (tpt) cc_final: 0.8564 (tpp) REVERT: H 72 ARG cc_start: 0.9706 (ttm170) cc_final: 0.9399 (ptm160) REVERT: H 80 LEU cc_start: 0.9739 (tp) cc_final: 0.9527 (tp) REVERT: H 99 ARG cc_start: 0.9591 (mtt90) cc_final: 0.8789 (ttm110) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2840 time to fit residues: 65.8659 Evaluate side-chains 131 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.022451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2298 r_free = 0.2298 target = 0.018721 restraints weight = 177125.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2333 r_free = 0.2333 target = 0.019470 restraints weight = 85434.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2357 r_free = 0.2357 target = 0.019981 restraints weight = 51319.747| |-----------------------------------------------------------------------------| r_work (final): 0.2352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13502 Z= 0.290 Angle : 0.699 14.269 19473 Z= 0.409 Chirality : 0.040 0.152 2213 Planarity : 0.005 0.071 1473 Dihedral : 34.754 133.623 4104 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 0.31 (0.29), residues: 838 helix: 1.00 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.29 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 87 HIS 0.009 0.001 HIS B 75 PHE 0.016 0.002 PHE A 102 TYR 0.025 0.002 TYR C 57 ARG 0.007 0.001 ARG D 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2084.06 seconds wall clock time: 41 minutes 25.23 seconds (2485.23 seconds total)