Starting phenix.real_space_refine on Fri Mar 15 19:57:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7by0_30239/03_2024/7by0_30239_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7by0_30239/03_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_30239/03_2024/7by0_30239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7by0_30239/03_2024/7by0_30239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7by0_30239/03_2024/7by0_30239_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7by0_30239/03_2024/7by0_30239_updated.pdb" } 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 Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "E ARG 118": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "K ARG 669": "NH1" <-> "NH2" Residue "L ARG 669": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.39, per 1000 atoms: 0.58 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 - 3.50 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: 7.84 Conformation dependent library (CDL) restraints added in 1.3 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... running ksdssp... Secondary structure from input PDB file: 36 helices and 0 sheets defined 59.3% alpha, 0.0% beta 140 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 7.53 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 65 through 79 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 89 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 124 through 134 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 48 through 75 removed outlier: 3.501A pdb=" N GLU B 52 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N THR B 54 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 58 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE B 66 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B 67 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.668A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 45 through 70 removed outlier: 4.491A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.513A pdb=" N HIS D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL D 111 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR D 122 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 65 through 79 removed outlier: 3.506A pdb=" N ILE E 75 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 116 removed outlier: 3.558A pdb=" N LEU E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 137 removed outlier: 4.403A pdb=" N GLY E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU E 136 " --> pdb=" O ARG E 132 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N GLN E 137 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 48 through 76 removed outlier: 3.609A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N THR F 54 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG F 67 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL F 70 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR F 73 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 73 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 80 through 89 removed outlier: 3.625A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 83 Processing helix chain 'H' and resid 91 through 101 removed outlier: 3.719A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 123 Processing helix chain 'K' and resid 629 through 639 removed outlier: 3.564A pdb=" N ASN K 634 " --> pdb=" O GLN K 631 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU K 635 " --> pdb=" O ILE K 632 " (cutoff:3.500A) Processing helix chain 'L' and resid 629 through 639 removed outlier: 3.584A pdb=" N ASN L 634 " --> pdb=" O GLN L 631 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU L 635 " --> pdb=" O ILE L 632 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 834 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: 5.10 Time building geometry restraints manager: 8.17 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: 95.99 - 103.68: 866 103.68 - 111.36: 6836 111.36 - 119.05: 4709 119.05 - 126.74: 6297 126.74 - 134.42: 765 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: 141 2.54 - 3.13: 9182 3.13 - 3.72: 26001 3.72 - 4.31: 32469 4.31 - 4.90: 45659 Nonbonded interactions: 113452 Sorted by model distance: nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG K 659 " model vdw 1.950 2.520 nonbonded pdb=" OE2 GLU G 92 " pdb=" NH1 ARG L 659 " model vdw 2.048 2.520 nonbonded pdb=" OE1 GLU D 105 " pdb=" N ILE K 660 " model vdw 2.206 2.520 nonbonded pdb=" OG SER G 40 " pdb=" O SER H 87 " model vdw 2.226 2.440 nonbonded pdb=" OG1 THR E 80 " pdb=" O VAL E 83 " model vdw 2.254 2.440 ... (remaining 113447 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.680 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: 2.660 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 44.740 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.730 ------------------------------------------------------------------------------- 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= 0.404 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 : 1.081 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: 0.3258 time to fit residues: 91.8942 Evaluate side-chains 141 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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: 10.0000 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 0.2980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 overall best weight: 5.6588 ------------------------------------------------------------------------------- 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 88 GLN A 96 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 95 GLN E 128 GLN F 64 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 68 ASN H 49 HIS K 650 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13502 Z= 0.299 Angle : 0.721 11.511 19473 Z= 0.430 Chirality : 0.042 0.221 2213 Planarity : 0.006 0.043 1473 Dihedral : 34.972 127.203 4104 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.15 % Allowed : 4.09 % 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: -1.45 (0.27), residues: 838 helix: -0.21 (0.21), residues: 520 sheet: None (None), residues: 0 loop : -2.17 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 668 HIS 0.006 0.001 HIS F 75 PHE 0.014 0.002 PHE E 68 TYR 0.013 0.002 TYR E 42 ARG 0.005 0.001 ARG H 86 *********************** 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 184 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.522 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: A 55 TYR cc_start: 0.9471 (m-10) cc_final: 0.9146 (m-10) REVERT: A 68 PHE cc_start: 0.9521 (t80) cc_final: 0.8955 (t80) REVERT: A 74 GLU cc_start: 0.8929 (tt0) cc_final: 0.8338 (mt-10) REVERT: A 85 TYR cc_start: 0.9523 (m-80) cc_final: 0.9087 (m-80) REVERT: A 96 GLN cc_start: 0.9196 (tp-100) cc_final: 0.8693 (tp40) REVERT: A 97 GLU cc_start: 0.9461 (mt-10) cc_final: 0.8883 (mt-10) REVERT: A 100 GLU cc_start: 0.9398 (mt-10) cc_final: 0.8935 (mt-10) REVERT: B 59 LYS cc_start: 0.9740 (ptmt) cc_final: 0.9509 (ptmm) REVERT: B 63 GLU cc_start: 0.9444 (mt-10) cc_final: 0.9130 (mp0) REVERT: B 74 GLU cc_start: 0.9419 (tm-30) cc_final: 0.9181 (tm-30) REVERT: B 84 MET cc_start: 0.9377 (mmm) cc_final: 0.9140 (mmt) REVERT: C 36 LYS cc_start: 0.9490 (mtpt) cc_final: 0.9059 (mmtp) REVERT: C 87 ILE cc_start: 0.9793 (mm) cc_final: 0.9423 (tp) REVERT: D 68 ASP cc_start: 0.9230 (t70) cc_final: 0.8923 (t0) REVERT: D 72 ARG cc_start: 0.9550 (ttm170) cc_final: 0.8925 (ptm160) REVERT: D 95 GLN cc_start: 0.9725 (tt0) cc_final: 0.9035 (tt0) REVERT: D 99 ARG cc_start: 0.9398 (mtt180) cc_final: 0.8780 (ttm110) REVERT: D 113 GLU cc_start: 0.9713 (mm-30) cc_final: 0.9310 (mm-30) REVERT: E 90 MET cc_start: 0.9257 (tmm) cc_final: 0.9015 (tmm) REVERT: E 95 LEU cc_start: 0.9899 (tp) cc_final: 0.9680 (pp) REVERT: E 97 GLU cc_start: 0.9349 (tt0) cc_final: 0.8894 (tt0) REVERT: E 128 GLN cc_start: 0.9678 (OUTLIER) cc_final: 0.9278 (mm-40) REVERT: F 60 VAL cc_start: 0.9635 (m) cc_final: 0.9292 (p) REVERT: F 63 GLU cc_start: 0.9507 (mt-10) cc_final: 0.9261 (mt-10) REVERT: F 74 GLU cc_start: 0.9608 (tt0) cc_final: 0.9192 (tm-30) REVERT: F 79 LYS cc_start: 0.9634 (mptt) cc_final: 0.9086 (ttpp) REVERT: F 84 MET cc_start: 0.9540 (mmp) cc_final: 0.9308 (mmm) REVERT: G 87 ILE cc_start: 0.9856 (mm) cc_final: 0.9525 (tp) REVERT: G 91 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8843 (mm-30) REVERT: G 92 GLU cc_start: 0.9270 (pm20) cc_final: 0.9020 (mt-10) REVERT: G 111 ILE cc_start: 0.9503 (tp) cc_final: 0.9271 (tp) REVERT: H 59 MET cc_start: 0.8944 (tpt) cc_final: 0.8614 (tpp) REVERT: H 72 ARG cc_start: 0.9622 (ttm170) cc_final: 0.9353 (ptm160) REVERT: H 80 LEU cc_start: 0.9625 (tp) cc_final: 0.9286 (tp) REVERT: H 99 ARG cc_start: 0.9549 (mtt90) cc_final: 0.8841 (ttm110) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.3092 time to fit residues: 76.4663 Evaluate side-chains 140 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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: 4.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 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: 4.7990 ------------------------------------------------------------------------------- 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 ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13502 Z= 0.262 Angle : 0.680 12.823 19473 Z= 0.406 Chirality : 0.040 0.168 2213 Planarity : 0.005 0.042 1473 Dihedral : 34.890 132.640 4104 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 4.82 % 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: -0.69 (0.28), residues: 838 helix: 0.32 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.74 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 668 HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE E 102 TYR 0.020 0.002 TYR G 39 ARG 0.008 0.001 ARG G 20 *********************** 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 183 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.146 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 68 PHE cc_start: 0.9530 (t80) cc_final: 0.9126 (t80) REVERT: A 74 GLU cc_start: 0.8979 (tt0) cc_final: 0.8382 (mt-10) REVERT: A 85 TYR cc_start: 0.9644 (m-80) cc_final: 0.9200 (m-80) REVERT: A 96 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8688 (tp40) REVERT: A 97 GLU cc_start: 0.9474 (mt-10) cc_final: 0.8861 (mt-10) REVERT: A 100 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8974 (mt-10) REVERT: B 53 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8854 (tm-30) REVERT: B 59 LYS cc_start: 0.9777 (ptmt) cc_final: 0.9478 (ptmm) REVERT: B 62 LEU cc_start: 0.9822 (mt) cc_final: 0.9581 (mt) REVERT: B 63 GLU cc_start: 0.9444 (mt-10) cc_final: 0.9172 (mp0) REVERT: B 74 GLU cc_start: 0.9471 (tm-30) cc_final: 0.9202 (tm-30) REVERT: B 84 MET cc_start: 0.9426 (mmm) cc_final: 0.9075 (mmm) REVERT: C 36 LYS cc_start: 0.9525 (mtpt) cc_final: 0.9025 (mmtp) REVERT: C 87 ILE cc_start: 0.9805 (mm) cc_final: 0.9432 (tp) REVERT: C 102 ILE cc_start: 0.9299 (tp) cc_final: 0.9011 (tt) REVERT: D 72 ARG cc_start: 0.9541 (ttm170) cc_final: 0.9333 (ptm160) REVERT: D 99 ARG cc_start: 0.9361 (mtt180) cc_final: 0.8790 (ttm110) REVERT: D 113 GLU cc_start: 0.9704 (mm-30) cc_final: 0.9360 (mm-30) REVERT: E 85 TYR cc_start: 0.9574 (m-10) cc_final: 0.9177 (m-80) REVERT: E 90 MET cc_start: 0.9278 (tmm) cc_final: 0.8987 (tmm) REVERT: E 95 LEU cc_start: 0.9900 (tp) cc_final: 0.9676 (pp) REVERT: E 128 GLN cc_start: 0.9691 (tt0) cc_final: 0.9312 (tp-100) REVERT: E 139 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8760 (mp0) REVERT: F 53 GLU cc_start: 0.9397 (tm-30) cc_final: 0.9005 (tm-30) REVERT: F 74 GLU cc_start: 0.9604 (tt0) cc_final: 0.9174 (tm-30) REVERT: F 79 LYS cc_start: 0.9594 (mptt) cc_final: 0.9136 (ttpp) REVERT: F 84 MET cc_start: 0.9568 (mmp) cc_final: 0.9343 (mmm) REVERT: G 87 ILE cc_start: 0.9844 (mm) cc_final: 0.9476 (tp) REVERT: G 95 LYS cc_start: 0.9660 (tttp) cc_final: 0.9357 (tptm) REVERT: H 59 MET cc_start: 0.8933 (tpt) cc_final: 0.8656 (tpp) REVERT: H 72 ARG cc_start: 0.9695 (ttm170) cc_final: 0.9247 (ptm160) REVERT: H 80 LEU cc_start: 0.9628 (tp) cc_final: 0.9300 (tp) REVERT: H 99 ARG cc_start: 0.9496 (mtt90) cc_final: 0.8798 (ttm110) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.3011 time to fit residues: 74.5185 Evaluate side-chains 138 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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: 3.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.1980 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 109 HIS ** E 96 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13502 Z= 0.213 Angle : 0.643 13.986 19473 Z= 0.382 Chirality : 0.039 0.163 2213 Planarity : 0.005 0.044 1473 Dihedral : 34.712 130.726 4104 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.15 % Allowed : 3.65 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.29), residues: 838 helix: 0.60 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.62 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 668 HIS 0.006 0.001 HIS B 75 PHE 0.014 0.001 PHE E 68 TYR 0.011 0.001 TYR E 55 ARG 0.007 0.000 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 183 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 1.199 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 68 PHE cc_start: 0.9497 (t80) cc_final: 0.9050 (t80) REVERT: A 74 GLU cc_start: 0.8980 (tt0) cc_final: 0.8461 (mt-10) REVERT: A 85 TYR cc_start: 0.9640 (m-80) cc_final: 0.9224 (m-80) REVERT: A 96 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8724 (tp40) REVERT: A 97 GLU cc_start: 0.9484 (mt-10) cc_final: 0.8893 (mt-10) REVERT: A 100 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8946 (mt-10) REVERT: A 109 ASP cc_start: 0.9164 (m-30) cc_final: 0.8796 (m-30) REVERT: A 137 GLN cc_start: 0.8821 (mp10) cc_final: 0.8586 (mp10) REVERT: B 53 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8821 (tm-30) REVERT: B 74 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9154 (tm-30) REVERT: B 84 MET cc_start: 0.9412 (mmm) cc_final: 0.9016 (mmm) REVERT: C 36 LYS cc_start: 0.9521 (mtpt) cc_final: 0.9020 (mmtp) REVERT: C 57 TYR cc_start: 0.9251 (t80) cc_final: 0.8891 (t80) REVERT: C 87 ILE cc_start: 0.9792 (mm) cc_final: 0.9437 (tp) REVERT: D 59 MET cc_start: 0.8801 (tpt) cc_final: 0.8576 (tpt) REVERT: D 99 ARG cc_start: 0.9377 (mtt180) cc_final: 0.8794 (ttm110) REVERT: D 113 GLU cc_start: 0.9693 (mm-30) cc_final: 0.9285 (mm-30) REVERT: E 85 TYR cc_start: 0.9557 (m-10) cc_final: 0.9131 (m-80) REVERT: E 90 MET cc_start: 0.9284 (tmm) cc_final: 0.8962 (tmm) REVERT: E 95 LEU cc_start: 0.9902 (tp) cc_final: 0.9638 (pp) REVERT: E 100 GLU cc_start: 0.9447 (pt0) cc_final: 0.9236 (pt0) REVERT: E 128 GLN cc_start: 0.9670 (tt0) cc_final: 0.9258 (tp-100) REVERT: F 53 GLU cc_start: 0.9323 (tm-30) cc_final: 0.8903 (tm-30) REVERT: F 62 LEU cc_start: 0.9868 (mm) cc_final: 0.9668 (mm) REVERT: F 66 ILE cc_start: 0.9814 (mt) cc_final: 0.9501 (tt) REVERT: F 74 GLU cc_start: 0.9590 (tt0) cc_final: 0.9107 (tm-30) REVERT: F 79 LYS cc_start: 0.9557 (mptt) cc_final: 0.9105 (ttpp) REVERT: G 73 ASN cc_start: 0.9315 (t0) cc_final: 0.9051 (m110) REVERT: G 95 LYS cc_start: 0.9660 (tttp) cc_final: 0.9372 (tptm) REVERT: H 37 TYR cc_start: 0.9411 (m-80) cc_final: 0.9068 (m-10) REVERT: H 59 MET cc_start: 0.9035 (tpt) cc_final: 0.8705 (tpp) REVERT: H 68 ASP cc_start: 0.9282 (t70) cc_final: 0.9070 (t0) REVERT: H 72 ARG cc_start: 0.9653 (ttm170) cc_final: 0.9131 (ptm160) REVERT: H 80 LEU cc_start: 0.9603 (tp) cc_final: 0.9299 (tp) REVERT: H 99 ARG cc_start: 0.9469 (mtt90) cc_final: 0.8750 (ttm110) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.3321 time to fit residues: 82.2423 Evaluate side-chains 135 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.931 ------------------------------------------------------------------------------- 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: 6.9990 chunk 1 optimal weight: 10.0000 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: 4.9990 chunk 95 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- 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** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN L 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 13502 Z= 0.377 Angle : 0.743 17.060 19473 Z= 0.435 Chirality : 0.042 0.227 2213 Planarity : 0.006 0.044 1473 Dihedral : 34.922 132.103 4104 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 28.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: -0.56 (0.28), residues: 838 helix: 0.32 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -1.47 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 87 HIS 0.009 0.002 HIS B 75 PHE 0.013 0.002 PHE D 65 TYR 0.013 0.002 TYR C 50 ARG 0.010 0.001 ARG L 661 *********************** 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 167 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.071 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: A 68 PHE cc_start: 0.9521 (t80) cc_final: 0.9085 (t80) REVERT: A 74 GLU cc_start: 0.9032 (tt0) cc_final: 0.8436 (mt-10) REVERT: A 85 TYR cc_start: 0.9645 (m-80) cc_final: 0.9214 (m-80) REVERT: A 97 GLU cc_start: 0.9506 (mt-10) cc_final: 0.9292 (mt-10) REVERT: B 53 GLU cc_start: 0.9328 (tm-30) cc_final: 0.8882 (tm-30) REVERT: B 62 LEU cc_start: 0.9828 (mt) cc_final: 0.9556 (mt) REVERT: B 74 GLU cc_start: 0.9534 (tm-30) cc_final: 0.9321 (tm-30) REVERT: B 84 MET cc_start: 0.9466 (mmm) cc_final: 0.9264 (mmp) REVERT: C 36 LYS cc_start: 0.9509 (mtpt) cc_final: 0.9028 (mmtp) REVERT: C 75 LYS cc_start: 0.9749 (mmtt) cc_final: 0.9544 (mmmm) REVERT: D 68 ASP cc_start: 0.9350 (t70) cc_final: 0.9002 (t0) REVERT: D 71 GLU cc_start: 0.9198 (pp20) cc_final: 0.8919 (pp20) REVERT: D 95 GLN cc_start: 0.9703 (tt0) cc_final: 0.9480 (tt0) REVERT: D 113 GLU cc_start: 0.9693 (mm-30) cc_final: 0.9315 (mm-30) REVERT: E 74 GLU cc_start: 0.9176 (pt0) cc_final: 0.8895 (pt0) REVERT: E 85 TYR cc_start: 0.9591 (m-10) cc_final: 0.9174 (m-80) REVERT: E 90 MET cc_start: 0.9327 (tmm) cc_final: 0.9031 (tmm) REVERT: E 100 GLU cc_start: 0.9396 (pt0) cc_final: 0.9153 (pt0) REVERT: E 128 GLN cc_start: 0.9646 (tt0) cc_final: 0.9035 (tp-100) REVERT: F 53 GLU cc_start: 0.9387 (tm-30) cc_final: 0.8943 (tm-30) REVERT: F 74 GLU cc_start: 0.9641 (tt0) cc_final: 0.9263 (tm-30) REVERT: F 79 LYS cc_start: 0.9546 (mptt) cc_final: 0.9097 (ttpp) REVERT: G 95 LYS cc_start: 0.9704 (tttp) cc_final: 0.9447 (tptm) REVERT: H 37 TYR cc_start: 0.9521 (m-80) cc_final: 0.9182 (m-10) REVERT: H 72 ARG cc_start: 0.9691 (ttm170) cc_final: 0.9481 (ttm170) REVERT: H 80 LEU cc_start: 0.9682 (tp) cc_final: 0.9453 (tp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2887 time to fit residues: 65.9094 Evaluate side-chains 120 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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: 4.9990 chunk 95 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13502 Z= 0.202 Angle : 0.658 15.151 19473 Z= 0.387 Chirality : 0.040 0.157 2213 Planarity : 0.005 0.073 1473 Dihedral : 34.749 132.236 4104 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: -0.17 (0.29), residues: 838 helix: 0.58 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -1.21 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 668 HIS 0.006 0.001 HIS B 75 PHE 0.012 0.001 PHE C 25 TYR 0.015 0.001 TYR F 98 ARG 0.007 0.000 ARG K 661 *********************** 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 182 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.069 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 74 GLU cc_start: 0.8952 (tt0) cc_final: 0.8442 (mt-10) REVERT: A 85 TYR cc_start: 0.9595 (m-80) cc_final: 0.9253 (m-80) REVERT: A 97 GLU cc_start: 0.9505 (mt-10) cc_final: 0.8991 (mt-10) REVERT: A 100 GLU cc_start: 0.9519 (mt-10) cc_final: 0.8995 (mt-10) REVERT: A 109 ASP cc_start: 0.9176 (m-30) cc_final: 0.8822 (m-30) REVERT: B 53 GLU cc_start: 0.9337 (tm-30) cc_final: 0.8806 (tm-30) REVERT: B 74 GLU cc_start: 0.9462 (tm-30) cc_final: 0.9214 (tm-30) REVERT: B 84 MET cc_start: 0.9423 (mmm) cc_final: 0.9216 (mmp) REVERT: C 36 LYS cc_start: 0.9518 (mtpt) cc_final: 0.9048 (mmtp) REVERT: D 59 MET cc_start: 0.8752 (tpt) cc_final: 0.8482 (tpt) REVERT: D 63 ASN cc_start: 0.9464 (m-40) cc_final: 0.9118 (m-40) REVERT: D 68 ASP cc_start: 0.9390 (t70) cc_final: 0.9061 (t0) REVERT: D 71 GLU cc_start: 0.9107 (pp20) cc_final: 0.8847 (pp20) REVERT: D 99 ARG cc_start: 0.9358 (mtt180) cc_final: 0.8786 (ttm110) REVERT: E 51 GLU cc_start: 0.9603 (mm-30) cc_final: 0.9387 (mm-30) REVERT: E 74 GLU cc_start: 0.9220 (pt0) cc_final: 0.8936 (pt0) REVERT: E 85 TYR cc_start: 0.9576 (m-10) cc_final: 0.9119 (m-80) REVERT: E 90 MET cc_start: 0.9290 (tmm) cc_final: 0.8981 (tmm) REVERT: E 95 LEU cc_start: 0.9874 (tt) cc_final: 0.9668 (pp) REVERT: E 128 GLN cc_start: 0.9682 (tt0) cc_final: 0.9104 (tp-100) REVERT: E 139 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8813 (mp0) REVERT: F 53 GLU cc_start: 0.9358 (tm-30) cc_final: 0.8895 (tm-30) REVERT: F 74 GLU cc_start: 0.9582 (tt0) cc_final: 0.9103 (tm-30) REVERT: F 79 LYS cc_start: 0.9550 (mptt) cc_final: 0.9041 (ttpp) REVERT: G 36 LYS cc_start: 0.9468 (mptt) cc_final: 0.9267 (mptt) REVERT: G 73 ASN cc_start: 0.9356 (t0) cc_final: 0.9059 (m110) REVERT: G 95 LYS cc_start: 0.9677 (tttp) cc_final: 0.9362 (tptm) REVERT: H 59 MET cc_start: 0.8927 (tpt) cc_final: 0.8667 (tpp) REVERT: H 80 LEU cc_start: 0.9589 (tp) cc_final: 0.9315 (tp) REVERT: H 99 ARG cc_start: 0.9471 (mtt90) cc_final: 0.8713 (ttm110) REVERT: L 661 ARG cc_start: 0.9220 (mpp-170) cc_final: 0.8915 (mpt180) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2975 time to fit residues: 73.3811 Evaluate side-chains 127 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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: 5.9990 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13502 Z= 0.229 Angle : 0.658 15.623 19473 Z= 0.384 Chirality : 0.039 0.210 2213 Planarity : 0.005 0.043 1473 Dihedral : 34.663 131.712 4104 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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 (0.29), residues: 838 helix: 0.65 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -1.10 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 668 HIS 0.006 0.001 HIS B 75 PHE 0.009 0.001 PHE A 68 TYR 0.015 0.001 TYR F 98 ARG 0.004 0.000 ARG G 20 *********************** 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 172 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.123 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: A 74 GLU cc_start: 0.8988 (tt0) cc_final: 0.8435 (mt-10) REVERT: A 85 TYR cc_start: 0.9603 (m-80) cc_final: 0.9235 (m-80) REVERT: A 97 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9012 (mt-10) REVERT: A 100 GLU cc_start: 0.9525 (mt-10) cc_final: 0.9006 (mt-10) REVERT: A 109 ASP cc_start: 0.9152 (m-30) cc_final: 0.8832 (m-30) REVERT: B 53 GLU cc_start: 0.9361 (tm-30) cc_final: 0.8813 (tm-30) REVERT: B 74 GLU cc_start: 0.9470 (tm-30) cc_final: 0.9229 (tm-30) REVERT: B 84 MET cc_start: 0.9425 (mmm) cc_final: 0.9215 (mmp) REVERT: C 36 LYS cc_start: 0.9519 (mtpt) cc_final: 0.9073 (mmtp) REVERT: C 57 TYR cc_start: 0.9130 (t80) cc_final: 0.8876 (t80) REVERT: D 68 ASP cc_start: 0.9400 (t70) cc_final: 0.9034 (t0) REVERT: D 71 GLU cc_start: 0.9173 (pp20) cc_final: 0.8831 (pp20) REVERT: D 99 ARG cc_start: 0.9391 (mtt180) cc_final: 0.8823 (ttm110) REVERT: D 113 GLU cc_start: 0.9619 (mm-30) cc_final: 0.9287 (mm-30) REVERT: E 68 PHE cc_start: 0.9467 (t80) cc_final: 0.9258 (t80) REVERT: E 74 GLU cc_start: 0.9222 (pt0) cc_final: 0.8923 (pt0) REVERT: E 85 TYR cc_start: 0.9594 (m-10) cc_final: 0.9113 (m-80) REVERT: E 90 MET cc_start: 0.9276 (tmm) cc_final: 0.8965 (tmm) REVERT: E 96 GLN cc_start: 0.8923 (tp40) cc_final: 0.8715 (tp40) REVERT: E 97 GLU cc_start: 0.9485 (tt0) cc_final: 0.9076 (tt0) REVERT: E 128 GLN cc_start: 0.9677 (tt0) cc_final: 0.9059 (tp-100) REVERT: E 139 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8744 (mp0) REVERT: F 53 GLU cc_start: 0.9383 (tm-30) cc_final: 0.8969 (tm-30) REVERT: F 74 GLU cc_start: 0.9599 (tt0) cc_final: 0.9116 (tm-30) REVERT: F 79 LYS cc_start: 0.9537 (mptt) cc_final: 0.9068 (ttpp) REVERT: G 73 ASN cc_start: 0.9342 (t0) cc_final: 0.9051 (m110) REVERT: G 95 LYS cc_start: 0.9676 (tttp) cc_final: 0.9373 (tptm) REVERT: H 59 MET cc_start: 0.9003 (tpt) cc_final: 0.8795 (tpp) REVERT: H 79 ARG cc_start: 0.9564 (ptp-110) cc_final: 0.9340 (ptp90) REVERT: H 80 LEU cc_start: 0.9659 (tp) cc_final: 0.9405 (tp) REVERT: H 99 ARG cc_start: 0.9493 (mtt90) cc_final: 0.8729 (ttm110) REVERT: L 661 ARG cc_start: 0.9210 (mpp-170) cc_final: 0.8909 (mpt180) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2737 time to fit residues: 64.9967 Evaluate side-chains 126 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 101 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** ** 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** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3970 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= 0.277 Angle : 0.673 15.514 19473 Z= 0.395 Chirality : 0.040 0.154 2213 Planarity : 0.005 0.045 1473 Dihedral : 34.702 131.794 4104 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -0.09 (0.29), residues: 838 helix: 0.60 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.08 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 668 HIS 0.008 0.002 HIS B 75 PHE 0.008 0.002 PHE F 100 TYR 0.017 0.001 TYR F 98 ARG 0.008 0.001 ARG K 656 *********************** 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 167 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.990 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: A 66 GLN cc_start: 0.9615 (tp-100) cc_final: 0.9239 (tp-100) REVERT: A 74 GLU cc_start: 0.9029 (tt0) cc_final: 0.8487 (mt-10) REVERT: A 85 TYR cc_start: 0.9617 (m-80) cc_final: 0.9220 (m-80) REVERT: A 97 GLU cc_start: 0.9475 (mt-10) cc_final: 0.8915 (mt-10) REVERT: A 100 GLU cc_start: 0.9524 (mt-10) cc_final: 0.8999 (mt-10) REVERT: A 109 ASP cc_start: 0.9148 (m-30) cc_final: 0.8823 (m-30) REVERT: B 53 GLU cc_start: 0.9380 (tm-30) cc_final: 0.8821 (tm-30) REVERT: B 74 GLU cc_start: 0.9502 (tm-30) cc_final: 0.9263 (tm-30) REVERT: B 84 MET cc_start: 0.9429 (mmm) cc_final: 0.9221 (mmp) REVERT: B 87 VAL cc_start: 0.9834 (t) cc_final: 0.9617 (t) REVERT: C 36 LYS cc_start: 0.9547 (mtpt) cc_final: 0.9252 (tmmt) REVERT: C 57 TYR cc_start: 0.9136 (t80) cc_final: 0.8848 (t80) REVERT: C 102 ILE cc_start: 0.9575 (tp) cc_final: 0.9329 (tt) REVERT: D 68 ASP cc_start: 0.9426 (t70) cc_final: 0.9029 (t0) REVERT: D 71 GLU cc_start: 0.9135 (pp20) cc_final: 0.8859 (pp20) REVERT: D 99 ARG cc_start: 0.9403 (mtt180) cc_final: 0.8847 (ttm110) REVERT: D 113 GLU cc_start: 0.9618 (mm-30) cc_final: 0.9282 (mm-30) REVERT: E 74 GLU cc_start: 0.9227 (pt0) cc_final: 0.8919 (pt0) REVERT: E 85 TYR cc_start: 0.9619 (m-10) cc_final: 0.9147 (m-80) REVERT: E 90 MET cc_start: 0.9304 (tmm) cc_final: 0.8967 (tmm) REVERT: E 96 GLN cc_start: 0.9101 (tp40) cc_final: 0.8723 (tp40) REVERT: E 97 GLU cc_start: 0.9469 (tt0) cc_final: 0.9073 (tt0) REVERT: E 128 GLN cc_start: 0.9674 (tt0) cc_final: 0.9059 (tp-100) REVERT: F 53 GLU cc_start: 0.9406 (tm-30) cc_final: 0.8925 (tm-30) REVERT: F 74 GLU cc_start: 0.9627 (tt0) cc_final: 0.9144 (tm-30) REVERT: G 95 LYS cc_start: 0.9699 (tttp) cc_final: 0.9413 (tptm) REVERT: H 79 ARG cc_start: 0.9607 (ptp-110) cc_final: 0.9382 (ptp90) REVERT: H 80 LEU cc_start: 0.9679 (tp) cc_final: 0.9451 (tp) REVERT: H 99 ARG cc_start: 0.9498 (mtt90) cc_final: 0.8769 (ttm110) REVERT: L 661 ARG cc_start: 0.9207 (mpp-170) cc_final: 0.8893 (mpt180) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2888 time to fit residues: 65.9679 Evaluate side-chains 124 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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: 30.0000 chunk 59 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 overall best weight: 5.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.4197 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= 0.300 Angle : 0.694 15.668 19473 Z= 0.407 Chirality : 0.040 0.152 2213 Planarity : 0.005 0.045 1473 Dihedral : 34.756 132.438 4104 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 25.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.29), residues: 838 helix: 0.49 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.01 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 87 HIS 0.008 0.002 HIS B 75 PHE 0.008 0.002 PHE D 65 TYR 0.015 0.002 TYR F 98 ARG 0.004 0.001 ARG K 661 *********************** 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 163 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.934 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: A 66 GLN cc_start: 0.9648 (tp-100) cc_final: 0.9279 (tp-100) REVERT: A 74 GLU cc_start: 0.9042 (tt0) cc_final: 0.8453 (mt-10) REVERT: A 85 TYR cc_start: 0.9583 (m-80) cc_final: 0.9104 (m-80) REVERT: A 97 GLU cc_start: 0.9441 (mt-10) cc_final: 0.8735 (tp30) REVERT: A 100 GLU cc_start: 0.9526 (mt-10) cc_final: 0.9072 (mt-10) REVERT: A 137 GLN cc_start: 0.9001 (mp10) cc_final: 0.8794 (mp10) REVERT: B 53 GLU cc_start: 0.9401 (tm-30) cc_final: 0.8876 (tm-30) REVERT: B 74 GLU cc_start: 0.9512 (tm-30) cc_final: 0.9280 (tm-30) REVERT: B 84 MET cc_start: 0.9464 (mmm) cc_final: 0.9261 (mmp) REVERT: B 91 LYS cc_start: 0.9676 (ptmt) cc_final: 0.9285 (pttp) REVERT: C 36 LYS cc_start: 0.9547 (mtpt) cc_final: 0.9319 (tmmt) REVERT: C 57 TYR cc_start: 0.9140 (t80) cc_final: 0.8837 (t80) REVERT: D 68 ASP cc_start: 0.9424 (t70) cc_final: 0.9017 (t0) REVERT: D 71 GLU cc_start: 0.9187 (pp20) cc_final: 0.8866 (pp20) REVERT: D 99 ARG cc_start: 0.9415 (mtt180) cc_final: 0.8854 (ttm110) REVERT: D 113 GLU cc_start: 0.9629 (mm-30) cc_final: 0.9276 (mm-30) REVERT: E 85 TYR cc_start: 0.9597 (m-10) cc_final: 0.9202 (m-80) REVERT: E 96 GLN cc_start: 0.9109 (tp40) cc_final: 0.8768 (tp40) REVERT: E 97 GLU cc_start: 0.9484 (tt0) cc_final: 0.9099 (tt0) REVERT: F 53 GLU cc_start: 0.9396 (tm-30) cc_final: 0.8987 (tm-30) REVERT: F 74 GLU cc_start: 0.9634 (tt0) cc_final: 0.9218 (tm-30) REVERT: G 95 LYS cc_start: 0.9703 (tttp) cc_final: 0.9374 (tptm) REVERT: H 79 ARG cc_start: 0.9628 (ptp-110) cc_final: 0.9417 (ptp90) REVERT: H 80 LEU cc_start: 0.9672 (tp) cc_final: 0.9460 (tp) REVERT: H 99 ARG cc_start: 0.9560 (mtt90) cc_final: 0.8767 (ttm110) REVERT: L 661 ARG cc_start: 0.9210 (mpp-170) cc_final: 0.8891 (mpt180) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2801 time to fit residues: 63.1341 Evaluate side-chains 118 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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: 3.9990 chunk 72 optimal weight: 10.0000 chunk 109 optimal weight: 0.3980 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 30.0000 chunk 69 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13502 Z= 0.222 Angle : 0.661 15.953 19473 Z= 0.386 Chirality : 0.040 0.159 2213 Planarity : 0.005 0.042 1473 Dihedral : 34.622 131.763 4104 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 21.62 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: 0.04 (0.29), residues: 838 helix: 0.61 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -0.82 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 668 HIS 0.006 0.001 HIS B 75 PHE 0.013 0.001 PHE A 102 TYR 0.016 0.001 TYR F 98 ARG 0.008 0.000 ARG B 92 ********************** 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 165 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.068 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: A 66 GLN cc_start: 0.9666 (tp-100) cc_final: 0.9268 (tp-100) REVERT: A 74 GLU cc_start: 0.9030 (tt0) cc_final: 0.8452 (mt-10) REVERT: A 85 TYR cc_start: 0.9545 (m-80) cc_final: 0.9021 (m-80) REVERT: A 97 GLU cc_start: 0.9463 (mt-10) cc_final: 0.8846 (pt0) REVERT: A 100 GLU cc_start: 0.9496 (mt-10) cc_final: 0.9052 (mt-10) REVERT: A 104 VAL cc_start: 0.9545 (m) cc_final: 0.9259 (p) REVERT: A 108 GLU cc_start: 0.9538 (pm20) cc_final: 0.9296 (pm20) REVERT: A 109 ASP cc_start: 0.9596 (m-30) cc_final: 0.9378 (m-30) REVERT: A 137 GLN cc_start: 0.8899 (mp10) cc_final: 0.8672 (mp10) REVERT: B 53 GLU cc_start: 0.9406 (tm-30) cc_final: 0.8807 (tm-30) REVERT: B 74 GLU cc_start: 0.9482 (tm-30) cc_final: 0.9256 (tm-30) REVERT: B 84 MET cc_start: 0.9449 (mmm) cc_final: 0.9232 (mmp) REVERT: B 91 LYS cc_start: 0.9544 (ptmt) cc_final: 0.9125 (pttp) REVERT: C 36 LYS cc_start: 0.9515 (mtpt) cc_final: 0.9070 (mmtp) REVERT: D 68 ASP cc_start: 0.9392 (t70) cc_final: 0.8985 (t0) REVERT: D 71 GLU cc_start: 0.9162 (pp20) cc_final: 0.8777 (pp20) REVERT: D 99 ARG cc_start: 0.9384 (mtt180) cc_final: 0.8817 (ttm110) REVERT: E 68 PHE cc_start: 0.9456 (t80) cc_final: 0.9251 (t80) REVERT: E 85 TYR cc_start: 0.9566 (m-10) cc_final: 0.9153 (m-80) REVERT: E 90 MET cc_start: 0.9567 (tpt) cc_final: 0.9219 (tpt) REVERT: E 96 GLN cc_start: 0.9102 (tp40) cc_final: 0.8705 (tp40) REVERT: E 97 GLU cc_start: 0.9473 (tt0) cc_final: 0.9063 (tt0) REVERT: E 139 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8723 (mp0) REVERT: F 53 GLU cc_start: 0.9388 (tm-30) cc_final: 0.8927 (tm-30) REVERT: F 74 GLU cc_start: 0.9599 (tt0) cc_final: 0.9110 (tm-30) REVERT: G 95 LYS cc_start: 0.9687 (tttp) cc_final: 0.9318 (tptm) REVERT: H 79 ARG cc_start: 0.9598 (ptp-110) cc_final: 0.9384 (ptp90) REVERT: H 80 LEU cc_start: 0.9672 (tp) cc_final: 0.9437 (tp) REVERT: H 99 ARG cc_start: 0.9492 (mtt90) cc_final: 0.8723 (ttm110) REVERT: L 661 ARG cc_start: 0.9253 (mpp-170) cc_final: 0.9014 (mpt180) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2791 time to fit residues: 63.9905 Evaluate side-chains 123 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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: 7.9990 chunk 24 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 11 optimal weight: 0.0270 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 overall best weight: 4.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.023124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.019404 restraints weight = 173644.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2372 r_free = 0.2372 target = 0.020181 restraints weight = 85479.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.020714 restraints weight = 51542.597| |-----------------------------------------------------------------------------| r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.4424 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= 0.253 Angle : 0.676 15.523 19473 Z= 0.395 Chirality : 0.039 0.155 2213 Planarity : 0.005 0.042 1473 Dihedral : 34.597 131.361 4104 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.29), residues: 838 helix: 0.56 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -0.78 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K 668 HIS 0.007 0.001 HIS B 75 PHE 0.015 0.002 PHE A 102 TYR 0.013 0.001 TYR F 98 ARG 0.012 0.000 ARG H 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2123.29 seconds wall clock time: 39 minutes 25.58 seconds (2365.58 seconds total)