Starting phenix.real_space_refine on Fri Mar 15 14:17:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sef_10154/03_2024/6sef_10154.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sef_10154/03_2024/6sef_10154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sef_10154/03_2024/6sef_10154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sef_10154/03_2024/6sef_10154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sef_10154/03_2024/6sef_10154.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sef_10154/03_2024/6sef_10154.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 10 5.16 5 C 6608 2.51 5 N 2235 2.21 5 O 2778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "E ARG 130": "NH1" <-> "NH2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 68": "OD1" <-> "OD2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "V ARG 522": "NH1" <-> "NH2" Residue "V ASP 529": "OD1" <-> "OD2" Residue "V GLU 536": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11919 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 812 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} 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: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 812 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "F" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 618 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 792 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "V" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 160 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Time building chain proxies: 6.46, per 1000 atoms: 0.54 Number of scatterers: 11919 At special positions: 0 Unit cell: (79.3, 120.9, 115.7, 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 10 16.00 P 288 15.00 O 2778 8.00 N 2235 7.00 C 6608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 70.8% alpha, 2.7% beta 143 base pairs and 246 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.663A pdb=" N LEU A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.625A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.588A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.529A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 4.113A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.559A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.713A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.721A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 122 removed outlier: 3.866A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.603A pdb=" N GLU E 50 " --> pdb=" O GLY E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.792A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR E 79 " --> pdb=" O CYS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 117 removed outlier: 3.751A pdb=" N LEU E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 4.075A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.683A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 52 removed outlier: 3.878A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 49 through 52' Processing helix chain 'F' and resid 53 through 76 removed outlier: 3.667A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.861A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 removed outlier: 4.079A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.530A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 38 through 49 removed outlier: 3.703A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.537A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.691A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.716A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 7.106A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.861A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 7.038A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.712A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.809A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 354 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 246 stacking parallelities Total time for adding SS restraints: 4.21 Time building geometry restraints manager: 7.08 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: 1964 1.33 - 1.45: 4370 1.45 - 1.56: 5801 1.56 - 1.68: 577 1.68 - 1.80: 18 Bond restraints: 12730 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.504 -0.082 3.00e-02 1.11e+03 7.40e+00 bond pdb=" CG1 ILE B 66 " pdb=" CD1 ILE B 66 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.44e+00 bond pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.40e+00 bond pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.476 -0.054 3.00e-02 1.11e+03 3.20e+00 bond pdb=" C3' DC J -58 " pdb=" O3' DC J -58 " ideal model delta sigma weight residual 1.422 1.476 -0.054 3.00e-02 1.11e+03 3.18e+00 ... (remaining 12725 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.18: 1844 106.18 - 113.15: 6761 113.15 - 120.11: 4944 120.11 - 127.07: 4220 127.07 - 134.03: 664 Bond angle restraints: 18433 Sorted by residual: angle pdb=" C ARG A 44 " pdb=" N GLN A 45 " pdb=" CA GLN A 45 " ideal model delta sigma weight residual 122.46 127.99 -5.53 1.41e+00 5.03e-01 1.54e+01 angle pdb=" C SER V 535 " pdb=" N GLU V 536 " pdb=" CA GLU V 536 " ideal model delta sigma weight residual 121.70 128.22 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sigma weight residual 120.20 125.48 -5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 112.49 116.53 -4.04 1.21e+00 6.83e-01 1.12e+01 angle pdb=" CG1 VAL H 39 " pdb=" CB VAL H 39 " pdb=" CG2 VAL H 39 " ideal model delta sigma weight residual 110.80 103.51 7.29 2.20e+00 2.07e-01 1.10e+01 ... (remaining 18428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.21: 5352 32.21 - 64.41: 1481 64.41 - 96.62: 25 96.62 - 128.83: 2 128.83 - 161.03: 4 Dihedral angle restraints: 6864 sinusoidal: 4702 harmonic: 2162 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 58.97 161.03 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 66.60 153.40 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" C4' DC J -58 " pdb=" C3' DC J -58 " pdb=" O3' DC J -58 " pdb=" P DT J -57 " ideal model delta sinusoidal sigma weight residual 220.00 86.54 133.46 1 3.50e+01 8.16e-04 1.32e+01 ... (remaining 6861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1326 0.045 - 0.090: 593 0.090 - 0.134: 128 0.134 - 0.179: 34 0.179 - 0.224: 5 Chirality restraints: 2086 Sorted by residual: chirality pdb=" CA ASP E 108 " pdb=" N ASP E 108 " pdb=" C ASP E 108 " pdb=" CB ASP E 108 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" P DT J -16 " pdb=" OP1 DT J -16 " pdb=" OP2 DT J -16 " pdb=" O5' DT J -16 " both_signs ideal model delta sigma weight residual True 2.35 -2.56 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL H 48 " pdb=" CA VAL H 48 " pdb=" CG1 VAL H 48 " pdb=" CG2 VAL H 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 2083 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG V 522 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C ARG V 522 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG V 522 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE V 523 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 98 " 0.017 2.00e-02 2.50e+03 1.60e-02 5.11e+00 pdb=" CG TYR F 98 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR F 98 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR F 98 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 98 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 98 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR F 98 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 98 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -69 " -0.028 2.00e-02 2.50e+03 1.34e-02 4.91e+00 pdb=" N9 DA I -69 " 0.033 2.00e-02 2.50e+03 pdb=" C8 DA I -69 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I -69 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -69 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -69 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -69 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -69 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -69 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -69 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I -69 " 0.002 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1777 2.76 - 3.29: 10088 3.29 - 3.83: 24215 3.83 - 4.36: 26986 4.36 - 4.90: 38283 Nonbonded interactions: 101349 Sorted by model distance: nonbonded pdb=" O2 DC I -64 " pdb=" N2 DG J 64 " model vdw 2.225 2.496 nonbonded pdb=" N2 DG I -58 " pdb=" O2 DC J 58 " model vdw 2.250 2.496 nonbonded pdb=" O2 DC I -56 " pdb=" N2 DG J 56 " model vdw 2.270 2.496 nonbonded pdb=" N2 DG I -60 " pdb=" O2 DC J 60 " model vdw 2.275 2.496 nonbonded pdb=" O2 DC I 5 " pdb=" N2 DG J -5 " model vdw 2.283 2.496 ... (remaining 101344 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' and resid 25 through 100) selection = (chain 'F' and resid 25 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 111) } ncs_group { reference = (chain 'D' and resid 35 through 124) selection = chain 'H' } 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 1.760 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 37.990 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 0.007 0.082 12730 Z= 0.388 Angle : 0.851 9.370 18433 Z= 0.493 Chirality : 0.052 0.224 2086 Planarity : 0.005 0.032 1322 Dihedral : 27.687 161.032 5470 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 16.08 % Favored : 83.92 % 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: -2.10 (0.26), residues: 733 helix: -0.93 (0.20), residues: 495 sheet: None (None), residues: 0 loop : -2.17 (0.33), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP V 530 HIS 0.009 0.002 HIS F 75 PHE 0.011 0.002 PHE H 65 TYR 0.038 0.003 TYR F 98 ARG 0.004 0.001 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8673 (mt-10) REVERT: A 52 ARG cc_start: 0.9226 (ttm170) cc_final: 0.8720 (mtm-85) REVERT: A 63 ARG cc_start: 0.8372 (mmp-170) cc_final: 0.8031 (mmm-85) REVERT: A 77 LYS cc_start: 0.9121 (ttmm) cc_final: 0.8862 (ttmm) REVERT: A 78 PHE cc_start: 0.8862 (m-80) cc_final: 0.7841 (m-80) REVERT: A 85 ASN cc_start: 0.9507 (m-40) cc_final: 0.9272 (m-40) REVERT: A 95 GLN cc_start: 0.9069 (tt0) cc_final: 0.8820 (tt0) REVERT: A 96 GLU cc_start: 0.8979 (tp30) cc_final: 0.8649 (tp30) REVERT: A 108 ASP cc_start: 0.8669 (m-30) cc_final: 0.8328 (p0) REVERT: B 30 THR cc_start: 0.8763 (p) cc_final: 0.8428 (t) REVERT: B 44 LYS cc_start: 0.9099 (tttm) cc_final: 0.8690 (mtpp) REVERT: B 51 TYR cc_start: 0.8980 (m-80) cc_final: 0.8429 (m-80) REVERT: B 64 ASN cc_start: 0.8608 (m-40) cc_final: 0.8407 (m110) REVERT: B 79 LYS cc_start: 0.8954 (mtmm) cc_final: 0.8603 (mtpp) REVERT: B 81 VAL cc_start: 0.9388 (t) cc_final: 0.9167 (t) REVERT: C 32 ARG cc_start: 0.9247 (ttp80) cc_final: 0.9032 (ptm-80) REVERT: C 36 LYS cc_start: 0.9609 (mptt) cc_final: 0.9367 (mmmm) REVERT: C 39 TYR cc_start: 0.8755 (m-80) cc_final: 0.8545 (m-80) REVERT: C 61 GLU cc_start: 0.9063 (tp30) cc_final: 0.8729 (tp30) REVERT: C 64 GLU cc_start: 0.8377 (tp30) cc_final: 0.7950 (tp30) REVERT: C 68 ASN cc_start: 0.8803 (m110) cc_final: 0.8171 (m110) REVERT: C 95 LYS cc_start: 0.9579 (ttmm) cc_final: 0.9179 (tptt) REVERT: C 102 ILE cc_start: 0.9320 (mm) cc_final: 0.9052 (mt) REVERT: D 35 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7572 (mm-30) REVERT: D 37 TYR cc_start: 0.9280 (m-80) cc_final: 0.9053 (m-80) REVERT: D 71 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8197 (tm-30) REVERT: D 83 TYR cc_start: 0.8258 (m-10) cc_final: 0.7946 (m-10) REVERT: D 95 GLN cc_start: 0.9197 (tt0) cc_final: 0.8928 (tm-30) REVERT: D 120 LYS cc_start: 0.9556 (tttt) cc_final: 0.9290 (ttmm) REVERT: E 53 LYS cc_start: 0.9442 (ttpt) cc_final: 0.8998 (pttp) REVERT: E 65 LEU cc_start: 0.9463 (tp) cc_final: 0.9188 (tp) REVERT: E 89 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8203 (mm-40) REVERT: E 107 GLU cc_start: 0.8419 (pt0) cc_final: 0.8025 (pt0) REVERT: E 130 ARG cc_start: 0.9576 (mtp180) cc_final: 0.9265 (mtp85) REVERT: E 137 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6945 (mm-30) REVERT: F 59 LYS cc_start: 0.8732 (tttm) cc_final: 0.8229 (tttm) REVERT: F 64 ASN cc_start: 0.9217 (t0) cc_final: 0.8753 (t0) REVERT: F 68 ASP cc_start: 0.8721 (m-30) cc_final: 0.7358 (m-30) REVERT: F 88 TYR cc_start: 0.8753 (m-10) cc_final: 0.8112 (m-80) REVERT: G 25 PHE cc_start: 0.8452 (m-80) cc_final: 0.8220 (m-10) REVERT: G 36 LYS cc_start: 0.9228 (mmmt) cc_final: 0.8946 (mmtt) REVERT: G 56 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8329 (tt0) REVERT: G 64 GLU cc_start: 0.8778 (tp30) cc_final: 0.7860 (tp30) REVERT: G 65 LEU cc_start: 0.9499 (mm) cc_final: 0.9258 (mm) REVERT: G 68 ASN cc_start: 0.8259 (m110) cc_final: 0.7177 (m110) REVERT: G 84 GLN cc_start: 0.9318 (tp-100) cc_final: 0.8391 (tp-100) REVERT: H 79 ARG cc_start: 0.8958 (ptp90) cc_final: 0.8586 (mtm110) REVERT: H 83 TYR cc_start: 0.8518 (m-10) cc_final: 0.7854 (m-10) REVERT: H 90 THR cc_start: 0.8840 (p) cc_final: 0.8266 (p) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.3428 time to fit residues: 139.0271 Evaluate side-chains 239 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 73 ASN D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS E 95 GLN G 38 ASN G 94 ASN H 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12730 Z= 0.249 Angle : 0.616 6.384 18433 Z= 0.361 Chirality : 0.034 0.206 2086 Planarity : 0.004 0.045 1322 Dihedral : 30.355 159.629 3997 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.38 % Allowed : 23.47 % Favored : 73.15 % 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 (0.30), residues: 733 helix: 0.72 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -1.75 (0.35), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.008 0.002 HIS D 82 PHE 0.018 0.001 PHE H 65 TYR 0.021 0.002 TYR E 110 ARG 0.005 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 262 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8546 (mt-10) REVERT: A 78 PHE cc_start: 0.8920 (m-80) cc_final: 0.8643 (m-80) REVERT: A 85 ASN cc_start: 0.9534 (m-40) cc_final: 0.9189 (m-40) REVERT: A 96 GLU cc_start: 0.8926 (tp30) cc_final: 0.8717 (tp30) REVERT: A 104 HIS cc_start: 0.8428 (t70) cc_final: 0.7725 (t70) REVERT: A 107 GLU cc_start: 0.8790 (pp20) cc_final: 0.8224 (pp20) REVERT: A 108 ASP cc_start: 0.8700 (m-30) cc_final: 0.7799 (m-30) REVERT: A 127 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8528 (tm-30) REVERT: B 30 THR cc_start: 0.9024 (p) cc_final: 0.8662 (t) REVERT: B 31 LYS cc_start: 0.9247 (mtpp) cc_final: 0.8758 (mtpp) REVERT: B 44 LYS cc_start: 0.9056 (tttm) cc_final: 0.8658 (mtpp) REVERT: B 79 LYS cc_start: 0.8937 (mtmm) cc_final: 0.8692 (ttmm) REVERT: B 81 VAL cc_start: 0.9458 (t) cc_final: 0.9247 (t) REVERT: B 88 TYR cc_start: 0.8880 (m-10) cc_final: 0.8414 (m-80) REVERT: C 32 ARG cc_start: 0.9244 (ttp80) cc_final: 0.8786 (ptm160) REVERT: C 68 ASN cc_start: 0.8773 (m-40) cc_final: 0.7800 (m110) REVERT: C 95 LYS cc_start: 0.9592 (ttmm) cc_final: 0.9226 (tptt) REVERT: C 104 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7389 (mm-40) REVERT: D 35 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7726 (mm-30) REVERT: D 37 TYR cc_start: 0.9455 (m-80) cc_final: 0.9141 (m-80) REVERT: D 71 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8457 (tm-30) REVERT: D 83 TYR cc_start: 0.8437 (m-10) cc_final: 0.7490 (m-10) REVERT: D 95 GLN cc_start: 0.9272 (tt0) cc_final: 0.9057 (tm-30) REVERT: D 105 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8385 (tm-30) REVERT: D 120 LYS cc_start: 0.9592 (tttt) cc_final: 0.9340 (ttmm) REVERT: E 65 LEU cc_start: 0.9499 (tp) cc_final: 0.9255 (tp) REVERT: E 74 ILE cc_start: 0.9609 (tt) cc_final: 0.9383 (tt) REVERT: E 89 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8214 (mm-40) REVERT: E 104 HIS cc_start: 0.9030 (t-90) cc_final: 0.8598 (t70) REVERT: E 107 GLU cc_start: 0.8263 (pt0) cc_final: 0.8032 (pt0) REVERT: E 130 ARG cc_start: 0.9616 (mtp180) cc_final: 0.9205 (mtp85) REVERT: F 52 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8491 (tp30) REVERT: F 55 ARG cc_start: 0.8182 (mpt-90) cc_final: 0.7931 (mpt-90) REVERT: F 74 GLU cc_start: 0.8979 (tp30) cc_final: 0.8753 (tp30) REVERT: F 88 TYR cc_start: 0.8841 (m-10) cc_final: 0.7894 (m-80) REVERT: G 25 PHE cc_start: 0.8408 (m-80) cc_final: 0.8184 (m-10) REVERT: G 36 LYS cc_start: 0.9196 (mmmt) cc_final: 0.8937 (mmtt) REVERT: G 64 GLU cc_start: 0.8697 (tp30) cc_final: 0.8330 (tp30) REVERT: G 65 LEU cc_start: 0.9607 (mm) cc_final: 0.9302 (mm) REVERT: G 84 GLN cc_start: 0.9310 (tp-100) cc_final: 0.8685 (tp-100) REVERT: G 95 LYS cc_start: 0.9067 (ttpt) cc_final: 0.8720 (ttmm) REVERT: H 46 LYS cc_start: 0.9148 (tppt) cc_final: 0.8917 (tppt) REVERT: H 83 TYR cc_start: 0.8480 (m-10) cc_final: 0.7775 (m-10) REVERT: H 100 LEU cc_start: 0.9327 (mt) cc_final: 0.9083 (mt) REVERT: H 105 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8510 (tm-30) outliers start: 21 outliers final: 13 residues processed: 268 average time/residue: 0.2818 time to fit residues: 100.6238 Evaluate side-chains 244 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 231 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 95 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12730 Z= 0.338 Angle : 0.633 5.578 18433 Z= 0.374 Chirality : 0.037 0.176 2086 Planarity : 0.004 0.041 1322 Dihedral : 30.564 161.122 3997 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.66 % Allowed : 26.05 % Favored : 69.29 % 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: 0.52 (0.30), residues: 733 helix: 1.16 (0.23), residues: 511 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 86 HIS 0.008 0.001 HIS D 109 PHE 0.016 0.002 PHE F 61 TYR 0.020 0.002 TYR G 39 ARG 0.004 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 246 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8602 (mt-10) REVERT: A 87 GLN cc_start: 0.9266 (mt0) cc_final: 0.9014 (mt0) REVERT: A 96 GLU cc_start: 0.8929 (tp30) cc_final: 0.8717 (tp30) REVERT: A 104 HIS cc_start: 0.8556 (t70) cc_final: 0.7651 (t70) REVERT: A 108 ASP cc_start: 0.8929 (m-30) cc_final: 0.7977 (m-30) REVERT: A 127 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8636 (tm-30) REVERT: B 30 THR cc_start: 0.9108 (p) cc_final: 0.8753 (t) REVERT: B 31 LYS cc_start: 0.9263 (mtpp) cc_final: 0.9043 (ttmm) REVERT: B 44 LYS cc_start: 0.9083 (tttm) cc_final: 0.8735 (mtpp) REVERT: B 51 TYR cc_start: 0.9070 (m-80) cc_final: 0.8820 (m-80) REVERT: B 79 LYS cc_start: 0.9000 (mtmm) cc_final: 0.8763 (ttmm) REVERT: C 32 ARG cc_start: 0.9269 (ttp80) cc_final: 0.8931 (ptm-80) REVERT: C 68 ASN cc_start: 0.8512 (m-40) cc_final: 0.8235 (m110) REVERT: C 91 GLU cc_start: 0.8613 (pm20) cc_final: 0.7490 (pm20) REVERT: C 95 LYS cc_start: 0.9615 (ttmm) cc_final: 0.9249 (tptt) REVERT: D 35 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7727 (mm-30) REVERT: D 47 GLN cc_start: 0.9261 (tm-30) cc_final: 0.8997 (tm-30) REVERT: D 71 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8542 (tm-30) REVERT: D 93 GLU cc_start: 0.8909 (mp0) cc_final: 0.8595 (mp0) REVERT: D 95 GLN cc_start: 0.9255 (tt0) cc_final: 0.8999 (tm-30) REVERT: D 105 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8275 (tm-30) REVERT: D 121 TYR cc_start: 0.9436 (t80) cc_final: 0.9105 (t80) REVERT: E 65 LEU cc_start: 0.9529 (tp) cc_final: 0.9260 (tp) REVERT: E 85 ASN cc_start: 0.8871 (m-40) cc_final: 0.8548 (m-40) REVERT: E 89 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8262 (mm-40) REVERT: E 104 HIS cc_start: 0.9120 (t-90) cc_final: 0.8639 (t70) REVERT: E 107 GLU cc_start: 0.8245 (pt0) cc_final: 0.8027 (pt0) REVERT: E 130 ARG cc_start: 0.9577 (mtp180) cc_final: 0.9123 (mtp85) REVERT: F 52 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8505 (tp30) REVERT: F 64 ASN cc_start: 0.9018 (t0) cc_final: 0.8798 (t0) REVERT: F 74 GLU cc_start: 0.9029 (tp30) cc_final: 0.8789 (tp30) REVERT: F 88 TYR cc_start: 0.8788 (m-10) cc_final: 0.8494 (m-80) REVERT: G 25 PHE cc_start: 0.8561 (m-80) cc_final: 0.8352 (m-10) REVERT: G 36 LYS cc_start: 0.9226 (mmmt) cc_final: 0.8898 (mmtt) REVERT: G 65 LEU cc_start: 0.9538 (mm) cc_final: 0.8908 (mm) REVERT: G 92 GLU cc_start: 0.8494 (tt0) cc_final: 0.7543 (tt0) REVERT: G 95 LYS cc_start: 0.9104 (ttpt) cc_final: 0.8838 (ttmm) REVERT: H 46 LYS cc_start: 0.9090 (tppt) cc_final: 0.8616 (tppt) REVERT: H 105 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7525 (tm-30) outliers start: 29 outliers final: 20 residues processed: 257 average time/residue: 0.2892 time to fit residues: 99.8219 Evaluate side-chains 248 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 228 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 89 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 104 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12730 Z= 0.237 Angle : 0.600 7.354 18433 Z= 0.354 Chirality : 0.035 0.163 2086 Planarity : 0.004 0.042 1322 Dihedral : 30.461 165.338 3997 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.22 % Allowed : 30.06 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.31), residues: 733 helix: 1.58 (0.23), residues: 507 sheet: None (None), residues: 0 loop : -1.34 (0.36), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.005 0.001 HIS F 75 PHE 0.012 0.001 PHE H 65 TYR 0.023 0.002 TYR D 83 ARG 0.005 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 245 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8529 (mt-10) REVERT: A 87 GLN cc_start: 0.9284 (mt0) cc_final: 0.9036 (mt0) REVERT: A 104 HIS cc_start: 0.8499 (t-90) cc_final: 0.7763 (t70) REVERT: A 107 GLU cc_start: 0.8882 (pp20) cc_final: 0.8272 (pp20) REVERT: A 108 ASP cc_start: 0.8642 (m-30) cc_final: 0.7790 (m-30) REVERT: A 127 GLN cc_start: 0.8961 (tm-30) cc_final: 0.8575 (tm-30) REVERT: B 30 THR cc_start: 0.9069 (p) cc_final: 0.8704 (t) REVERT: B 79 LYS cc_start: 0.9007 (mtmm) cc_final: 0.8763 (ttmm) REVERT: B 88 TYR cc_start: 0.8895 (m-10) cc_final: 0.8694 (m-10) REVERT: C 32 ARG cc_start: 0.9250 (ttp80) cc_final: 0.8915 (ptm-80) REVERT: C 39 TYR cc_start: 0.8755 (m-80) cc_final: 0.8373 (m-80) REVERT: C 64 GLU cc_start: 0.8517 (tp30) cc_final: 0.8171 (tp30) REVERT: C 68 ASN cc_start: 0.8770 (m-40) cc_final: 0.8518 (m110) REVERT: C 90 ASP cc_start: 0.8603 (t70) cc_final: 0.7552 (t70) REVERT: C 95 LYS cc_start: 0.9604 (ttmm) cc_final: 0.9197 (tptt) REVERT: C 104 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7910 (tp-100) REVERT: D 35 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7820 (mm-30) REVERT: D 47 GLN cc_start: 0.9289 (tm-30) cc_final: 0.9018 (tm-30) REVERT: D 71 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8519 (tm-30) REVERT: D 93 GLU cc_start: 0.8831 (mp0) cc_final: 0.8493 (mp0) REVERT: D 95 GLN cc_start: 0.9202 (tt0) cc_final: 0.8941 (tm-30) REVERT: D 121 TYR cc_start: 0.9409 (t80) cc_final: 0.9129 (t80) REVERT: E 65 LEU cc_start: 0.9508 (tp) cc_final: 0.9228 (tp) REVERT: E 73 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8521 (tm-30) REVERT: E 104 HIS cc_start: 0.9067 (t-90) cc_final: 0.8532 (t70) REVERT: E 130 ARG cc_start: 0.9614 (mtp180) cc_final: 0.9308 (ptm160) REVERT: F 52 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8359 (tp30) REVERT: F 74 GLU cc_start: 0.9061 (tp30) cc_final: 0.8855 (tp30) REVERT: F 88 TYR cc_start: 0.8731 (m-10) cc_final: 0.7875 (m-80) REVERT: G 36 LYS cc_start: 0.9201 (mmmt) cc_final: 0.8843 (mmtt) REVERT: G 92 GLU cc_start: 0.8368 (tt0) cc_final: 0.7711 (tt0) REVERT: G 95 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8828 (ttmm) REVERT: H 46 LYS cc_start: 0.9154 (tppt) cc_final: 0.8658 (tppt) REVERT: H 83 TYR cc_start: 0.8474 (m-10) cc_final: 0.7487 (m-10) REVERT: H 86 ARG cc_start: 0.8929 (tpp80) cc_final: 0.8702 (tpp80) REVERT: H 105 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8028 (tm-30) REVERT: H 120 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8837 (tmtt) outliers start: 20 outliers final: 13 residues processed: 249 average time/residue: 0.2830 time to fit residues: 94.9586 Evaluate side-chains 243 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 230 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 93 GLN ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12730 Z= 0.276 Angle : 0.621 8.418 18433 Z= 0.364 Chirality : 0.036 0.150 2086 Planarity : 0.004 0.043 1322 Dihedral : 30.562 168.788 3997 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.02 % Allowed : 30.55 % Favored : 65.43 % 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: 1.26 (0.31), residues: 733 helix: 1.74 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.31 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.005 0.001 HIS F 75 PHE 0.010 0.001 PHE A 78 TYR 0.033 0.002 TYR D 83 ARG 0.007 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 242 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8532 (mt-10) REVERT: A 74 ILE cc_start: 0.9592 (tt) cc_final: 0.9330 (tt) REVERT: A 87 GLN cc_start: 0.9319 (mt0) cc_final: 0.9027 (mt0) REVERT: A 104 HIS cc_start: 0.8446 (t-90) cc_final: 0.7951 (t70) REVERT: A 107 GLU cc_start: 0.8808 (pp20) cc_final: 0.8366 (pp20) REVERT: A 108 ASP cc_start: 0.8157 (m-30) cc_final: 0.7286 (m-30) REVERT: A 110 TYR cc_start: 0.8994 (t80) cc_final: 0.8792 (t80) REVERT: A 122 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: A 127 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8677 (tm-30) REVERT: B 30 THR cc_start: 0.9071 (p) cc_final: 0.8795 (t) REVERT: B 44 LYS cc_start: 0.9046 (tttm) cc_final: 0.8660 (mtpp) REVERT: B 79 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8739 (ttmm) REVERT: C 32 ARG cc_start: 0.9266 (ttp80) cc_final: 0.8932 (ptm-80) REVERT: C 39 TYR cc_start: 0.8787 (m-80) cc_final: 0.8576 (m-80) REVERT: C 64 GLU cc_start: 0.8528 (tp30) cc_final: 0.8221 (tp30) REVERT: C 68 ASN cc_start: 0.8824 (m-40) cc_final: 0.8512 (m-40) REVERT: C 90 ASP cc_start: 0.8202 (t70) cc_final: 0.7884 (t70) REVERT: C 95 LYS cc_start: 0.9623 (ttmm) cc_final: 0.9238 (tptt) REVERT: C 104 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7918 (tp-100) REVERT: D 35 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7781 (mm-30) REVERT: D 47 GLN cc_start: 0.9321 (tm-30) cc_final: 0.9020 (tm-30) REVERT: D 71 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8489 (tm-30) REVERT: D 95 GLN cc_start: 0.9245 (tt0) cc_final: 0.8989 (tm-30) REVERT: D 121 TYR cc_start: 0.9430 (t80) cc_final: 0.9171 (t80) REVERT: E 65 LEU cc_start: 0.9528 (tp) cc_final: 0.9316 (tp) REVERT: E 73 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8606 (tm-30) REVERT: E 104 HIS cc_start: 0.9006 (t-90) cc_final: 0.8569 (t70) REVERT: E 130 ARG cc_start: 0.9595 (mtp180) cc_final: 0.9268 (ptm160) REVERT: F 52 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8389 (tp30) REVERT: F 74 GLU cc_start: 0.9003 (tp30) cc_final: 0.8782 (tp30) REVERT: F 88 TYR cc_start: 0.8740 (m-10) cc_final: 0.7666 (m-80) REVERT: G 36 LYS cc_start: 0.9216 (mmmt) cc_final: 0.8849 (mmtt) REVERT: G 65 LEU cc_start: 0.9611 (mm) cc_final: 0.9366 (mm) REVERT: G 92 GLU cc_start: 0.8405 (tt0) cc_final: 0.8066 (tt0) REVERT: G 95 LYS cc_start: 0.9136 (ttpt) cc_final: 0.8843 (ttmm) REVERT: H 46 LYS cc_start: 0.9095 (tppt) cc_final: 0.8543 (tppt) REVERT: H 83 TYR cc_start: 0.8539 (m-10) cc_final: 0.7593 (m-10) REVERT: H 120 LYS cc_start: 0.9038 (tmtt) cc_final: 0.8709 (tmtt) outliers start: 25 outliers final: 22 residues processed: 249 average time/residue: 0.2867 time to fit residues: 95.2517 Evaluate side-chains 251 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 228 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 91 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 95 GLN D 82 HIS ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12730 Z= 0.350 Angle : 0.666 9.623 18433 Z= 0.388 Chirality : 0.038 0.150 2086 Planarity : 0.004 0.043 1322 Dihedral : 30.769 174.911 3997 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.31 % Allowed : 31.35 % Favored : 63.34 % 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: 1.17 (0.31), residues: 733 helix: 1.69 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.40 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.007 0.001 HIS F 75 PHE 0.012 0.002 PHE H 70 TYR 0.042 0.003 TYR B 88 ARG 0.008 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 235 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8516 (mt-10) REVERT: A 74 ILE cc_start: 0.9543 (tt) cc_final: 0.9256 (tt) REVERT: A 87 GLN cc_start: 0.9356 (mt0) cc_final: 0.9104 (mt0) REVERT: A 104 HIS cc_start: 0.8516 (t-90) cc_final: 0.8129 (t70) REVERT: A 107 GLU cc_start: 0.8782 (pp20) cc_final: 0.8372 (pp20) REVERT: A 108 ASP cc_start: 0.8341 (m-30) cc_final: 0.7596 (m-30) REVERT: A 122 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8306 (m-80) REVERT: A 127 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8703 (tm-30) REVERT: B 27 GLN cc_start: 0.9172 (tp40) cc_final: 0.8972 (tp40) REVERT: B 30 THR cc_start: 0.9086 (p) cc_final: 0.8871 (t) REVERT: B 31 LYS cc_start: 0.9287 (ttmm) cc_final: 0.8991 (ttmm) REVERT: B 44 LYS cc_start: 0.9118 (tttm) cc_final: 0.8686 (mtpp) REVERT: B 51 TYR cc_start: 0.8963 (m-80) cc_final: 0.8621 (m-80) REVERT: B 79 LYS cc_start: 0.9032 (mtmm) cc_final: 0.8770 (ttmm) REVERT: C 32 ARG cc_start: 0.9335 (ttp80) cc_final: 0.8945 (ptm-80) REVERT: C 39 TYR cc_start: 0.8860 (m-80) cc_final: 0.8651 (m-80) REVERT: C 64 GLU cc_start: 0.8579 (tp30) cc_final: 0.8210 (tp30) REVERT: C 68 ASN cc_start: 0.8903 (m-40) cc_final: 0.8529 (m-40) REVERT: C 90 ASP cc_start: 0.8016 (t70) cc_final: 0.7812 (t70) REVERT: C 95 LYS cc_start: 0.9647 (ttmm) cc_final: 0.9214 (tptt) REVERT: C 104 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7963 (tp-100) REVERT: D 35 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7805 (mm-30) REVERT: D 37 TYR cc_start: 0.9551 (m-80) cc_final: 0.9337 (m-10) REVERT: D 47 GLN cc_start: 0.9349 (tm-30) cc_final: 0.9011 (tm-30) REVERT: D 71 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8514 (tm-30) REVERT: D 80 LEU cc_start: 0.9516 (tp) cc_final: 0.9292 (tp) REVERT: D 86 ARG cc_start: 0.8585 (tpp-160) cc_final: 0.8157 (tpp80) REVERT: D 93 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8716 (mm-30) REVERT: D 95 GLN cc_start: 0.9235 (tt0) cc_final: 0.8949 (tm-30) REVERT: E 73 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8678 (tm-30) REVERT: E 104 HIS cc_start: 0.9008 (t-90) cc_final: 0.8596 (t70) REVERT: E 130 ARG cc_start: 0.9604 (mtp180) cc_final: 0.9273 (ptm160) REVERT: F 52 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8471 (tp30) REVERT: F 72 TYR cc_start: 0.9217 (m-80) cc_final: 0.8969 (m-80) REVERT: F 84 MET cc_start: 0.8227 (tpp) cc_final: 0.7909 (tpp) REVERT: F 88 TYR cc_start: 0.8663 (m-10) cc_final: 0.7394 (m-80) REVERT: G 36 LYS cc_start: 0.9203 (mmmt) cc_final: 0.8857 (mmtt) REVERT: G 95 LYS cc_start: 0.9138 (ttpt) cc_final: 0.8787 (ttmm) REVERT: H 83 TYR cc_start: 0.8541 (m-10) cc_final: 0.7644 (m-10) REVERT: H 105 GLU cc_start: 0.8840 (tp30) cc_final: 0.8579 (tp30) REVERT: H 120 LYS cc_start: 0.9095 (tmtt) cc_final: 0.8760 (tmtt) outliers start: 33 outliers final: 24 residues processed: 246 average time/residue: 0.2789 time to fit residues: 92.0494 Evaluate side-chains 249 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 224 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12730 Z= 0.220 Angle : 0.636 10.876 18433 Z= 0.367 Chirality : 0.035 0.157 2086 Planarity : 0.004 0.046 1322 Dihedral : 30.569 177.188 3997 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.38 % Allowed : 33.92 % Favored : 62.70 % 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: 1.21 (0.31), residues: 733 helix: 1.68 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.28 (0.37), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 47 HIS 0.005 0.001 HIS D 82 PHE 0.011 0.001 PHE H 65 TYR 0.050 0.003 TYR B 88 ARG 0.008 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 243 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8439 (mt-10) REVERT: A 74 ILE cc_start: 0.9519 (tt) cc_final: 0.9252 (tt) REVERT: A 87 GLN cc_start: 0.9339 (mt0) cc_final: 0.9045 (mt0) REVERT: A 104 HIS cc_start: 0.8372 (t-90) cc_final: 0.7812 (t70) REVERT: A 107 GLU cc_start: 0.8769 (pp20) cc_final: 0.8102 (pp20) REVERT: A 108 ASP cc_start: 0.8138 (m-30) cc_final: 0.7186 (m-30) REVERT: A 122 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: A 127 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8651 (tm-30) REVERT: B 79 LYS cc_start: 0.9024 (mtmm) cc_final: 0.8717 (ttmm) REVERT: C 32 ARG cc_start: 0.9305 (ttp80) cc_final: 0.9065 (ptm-80) REVERT: C 39 TYR cc_start: 0.8736 (m-80) cc_final: 0.8528 (m-80) REVERT: C 64 GLU cc_start: 0.8581 (tp30) cc_final: 0.8306 (tp30) REVERT: C 95 LYS cc_start: 0.9613 (ttmm) cc_final: 0.9190 (tptt) REVERT: C 104 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7884 (tp-100) REVERT: D 35 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7945 (mm-30) REVERT: D 37 TYR cc_start: 0.9502 (m-80) cc_final: 0.9279 (m-10) REVERT: D 47 GLN cc_start: 0.9323 (tm-30) cc_final: 0.8977 (tm-30) REVERT: D 71 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8496 (tm-30) REVERT: D 80 LEU cc_start: 0.9468 (tp) cc_final: 0.9221 (tp) REVERT: D 86 ARG cc_start: 0.8321 (tpp-160) cc_final: 0.7801 (tpp80) REVERT: D 93 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8582 (mm-30) REVERT: D 95 GLN cc_start: 0.9250 (tt0) cc_final: 0.8984 (tm-30) REVERT: E 85 ASN cc_start: 0.8978 (m-40) cc_final: 0.8709 (m-40) REVERT: E 104 HIS cc_start: 0.9076 (t-90) cc_final: 0.8611 (t70) REVERT: E 130 ARG cc_start: 0.9628 (mtp180) cc_final: 0.9323 (ptm160) REVERT: F 52 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8385 (tp30) REVERT: F 84 MET cc_start: 0.8254 (tpp) cc_final: 0.7917 (tpp) REVERT: F 88 TYR cc_start: 0.8591 (m-10) cc_final: 0.7892 (m-80) REVERT: G 36 LYS cc_start: 0.9194 (mmmt) cc_final: 0.8808 (mmtt) REVERT: G 64 GLU cc_start: 0.8689 (tp30) cc_final: 0.8477 (tp30) REVERT: G 95 LYS cc_start: 0.9054 (ttpt) cc_final: 0.8698 (tppt) REVERT: H 46 LYS cc_start: 0.9208 (tppt) cc_final: 0.8697 (tppt) REVERT: H 83 TYR cc_start: 0.8461 (m-10) cc_final: 0.7827 (m-10) REVERT: H 116 LYS cc_start: 0.9565 (mtpp) cc_final: 0.9227 (mtpp) REVERT: H 120 LYS cc_start: 0.9098 (tmtt) cc_final: 0.8792 (tmtt) outliers start: 21 outliers final: 18 residues processed: 248 average time/residue: 0.2802 time to fit residues: 93.5338 Evaluate side-chains 246 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 227 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12730 Z= 0.244 Angle : 0.646 12.152 18433 Z= 0.371 Chirality : 0.035 0.156 2086 Planarity : 0.004 0.046 1322 Dihedral : 30.595 179.362 3997 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.02 % Allowed : 34.57 % Favored : 61.41 % 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: 1.12 (0.31), residues: 733 helix: 1.61 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.31 (0.37), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 47 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE F 61 TYR 0.059 0.002 TYR B 88 ARG 0.009 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 231 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8429 (mt-10) REVERT: A 74 ILE cc_start: 0.9533 (tt) cc_final: 0.9250 (tt) REVERT: A 87 GLN cc_start: 0.9349 (mt0) cc_final: 0.9073 (mt0) REVERT: A 104 HIS cc_start: 0.8467 (t-90) cc_final: 0.8001 (t70) REVERT: A 107 GLU cc_start: 0.8783 (pp20) cc_final: 0.8119 (pp20) REVERT: A 108 ASP cc_start: 0.8260 (m-30) cc_final: 0.7447 (m-30) REVERT: A 122 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8293 (m-80) REVERT: A 127 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8671 (tm-30) REVERT: B 31 LYS cc_start: 0.9214 (ttmm) cc_final: 0.8867 (ttmm) REVERT: B 51 TYR cc_start: 0.8823 (m-80) cc_final: 0.8615 (m-80) REVERT: B 79 LYS cc_start: 0.9026 (mtmm) cc_final: 0.8749 (ttmm) REVERT: B 84 MET cc_start: 0.8658 (tpp) cc_final: 0.8241 (tpp) REVERT: C 32 ARG cc_start: 0.9318 (ttp80) cc_final: 0.9075 (ptm-80) REVERT: C 39 TYR cc_start: 0.8747 (m-80) cc_final: 0.8369 (m-80) REVERT: C 56 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8379 (mm-30) REVERT: C 64 GLU cc_start: 0.8563 (tp30) cc_final: 0.8293 (tp30) REVERT: C 95 LYS cc_start: 0.9608 (ttmm) cc_final: 0.9185 (tptt) REVERT: C 104 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7884 (tp-100) REVERT: D 35 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7853 (mm-30) REVERT: D 37 TYR cc_start: 0.9503 (m-80) cc_final: 0.9287 (m-10) REVERT: D 42 TYR cc_start: 0.8295 (t80) cc_final: 0.8082 (t80) REVERT: D 47 GLN cc_start: 0.9348 (tm-30) cc_final: 0.8997 (tm-30) REVERT: D 71 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8476 (tm-30) REVERT: D 80 LEU cc_start: 0.9444 (tp) cc_final: 0.9176 (tp) REVERT: D 86 ARG cc_start: 0.8276 (tpp-160) cc_final: 0.7999 (tpp80) REVERT: D 93 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8549 (mm-30) REVERT: D 95 GLN cc_start: 0.9246 (tt0) cc_final: 0.8969 (tm-30) REVERT: E 85 ASN cc_start: 0.8989 (m-40) cc_final: 0.8716 (m-40) REVERT: E 104 HIS cc_start: 0.8969 (t-90) cc_final: 0.8547 (t70) REVERT: E 130 ARG cc_start: 0.9594 (mtp180) cc_final: 0.9313 (ptm160) REVERT: F 52 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8439 (tp30) REVERT: F 84 MET cc_start: 0.8258 (tpp) cc_final: 0.7922 (tpp) REVERT: F 88 TYR cc_start: 0.8606 (m-10) cc_final: 0.7988 (m-80) REVERT: G 36 LYS cc_start: 0.9207 (mmmt) cc_final: 0.8633 (mmmt) REVERT: G 95 LYS cc_start: 0.8996 (ttpt) cc_final: 0.8660 (tppt) REVERT: H 46 LYS cc_start: 0.9108 (tppt) cc_final: 0.8563 (tppt) REVERT: H 83 TYR cc_start: 0.8449 (m-10) cc_final: 0.7880 (m-10) REVERT: H 116 LYS cc_start: 0.9566 (mtpp) cc_final: 0.9229 (mtpp) REVERT: H 120 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8814 (tmtt) outliers start: 25 outliers final: 17 residues processed: 239 average time/residue: 0.2701 time to fit residues: 86.7300 Evaluate side-chains 240 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 221 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 95 GLN D 109 HIS ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 12730 Z= 0.322 Angle : 0.684 12.803 18433 Z= 0.392 Chirality : 0.038 0.154 2086 Planarity : 0.004 0.044 1322 Dihedral : 30.809 175.365 3997 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.34 % Allowed : 33.28 % Favored : 62.38 % 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: 1.04 (0.31), residues: 733 helix: 1.53 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.30 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.006 0.001 HIS F 75 PHE 0.012 0.002 PHE F 61 TYR 0.052 0.003 TYR D 83 ARG 0.010 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8438 (mt-10) REVERT: A 74 ILE cc_start: 0.9510 (tt) cc_final: 0.9230 (tt) REVERT: A 87 GLN cc_start: 0.9392 (mt0) cc_final: 0.9134 (mt0) REVERT: A 95 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8894 (tt0) REVERT: A 104 HIS cc_start: 0.8489 (t-90) cc_final: 0.8100 (t70) REVERT: A 107 GLU cc_start: 0.8803 (pp20) cc_final: 0.8413 (pp20) REVERT: A 108 ASP cc_start: 0.8377 (m-30) cc_final: 0.7657 (m-30) REVERT: A 122 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8310 (m-80) REVERT: A 127 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8673 (tm-30) REVERT: B 44 LYS cc_start: 0.9003 (tttm) cc_final: 0.8754 (mtpp) REVERT: B 68 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.7994 (t0) REVERT: B 79 LYS cc_start: 0.9025 (mtmm) cc_final: 0.8755 (ttmm) REVERT: B 84 MET cc_start: 0.8661 (tpp) cc_final: 0.8087 (tpp) REVERT: C 32 ARG cc_start: 0.9341 (ttp80) cc_final: 0.8814 (ptm-80) REVERT: C 39 TYR cc_start: 0.8813 (m-80) cc_final: 0.8569 (m-80) REVERT: C 56 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8395 (mm-30) REVERT: C 64 GLU cc_start: 0.8557 (tp30) cc_final: 0.8302 (tp30) REVERT: C 95 LYS cc_start: 0.9635 (ttmm) cc_final: 0.9209 (tptt) REVERT: C 104 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7949 (tp-100) REVERT: D 35 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7857 (mm-30) REVERT: D 37 TYR cc_start: 0.9527 (m-80) cc_final: 0.9298 (m-10) REVERT: D 47 GLN cc_start: 0.9364 (tm-30) cc_final: 0.9010 (tm-30) REVERT: D 71 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8500 (tm-30) REVERT: D 86 ARG cc_start: 0.8327 (tpp-160) cc_final: 0.8051 (tpp80) REVERT: D 93 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8587 (mm-30) REVERT: D 95 GLN cc_start: 0.9233 (tt0) cc_final: 0.8932 (tm-30) REVERT: E 104 HIS cc_start: 0.8994 (t-90) cc_final: 0.8572 (t70) REVERT: E 130 ARG cc_start: 0.9610 (mtp180) cc_final: 0.9314 (ptm160) REVERT: F 52 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8481 (tp30) REVERT: F 84 MET cc_start: 0.8333 (tpp) cc_final: 0.7987 (tpp) REVERT: F 88 TYR cc_start: 0.8619 (m-10) cc_final: 0.7951 (m-80) REVERT: G 36 LYS cc_start: 0.9202 (mmmt) cc_final: 0.8650 (mmmt) REVERT: G 39 TYR cc_start: 0.8815 (m-80) cc_final: 0.8513 (m-80) REVERT: G 95 LYS cc_start: 0.9051 (ttpt) cc_final: 0.8678 (ttmm) REVERT: H 46 LYS cc_start: 0.9077 (tppt) cc_final: 0.8475 (tppt) REVERT: H 83 TYR cc_start: 0.8506 (m-10) cc_final: 0.7905 (m-10) REVERT: H 120 LYS cc_start: 0.9167 (tmtt) cc_final: 0.8856 (tmtt) outliers start: 27 outliers final: 17 residues processed: 235 average time/residue: 0.2893 time to fit residues: 90.4051 Evaluate side-chains 242 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 221 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 0.0270 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN D 82 HIS D 109 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12730 Z= 0.227 Angle : 0.661 13.004 18433 Z= 0.378 Chirality : 0.036 0.166 2086 Planarity : 0.004 0.047 1322 Dihedral : 30.668 172.181 3997 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.18 % Allowed : 33.28 % Favored : 62.54 % 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: 1.11 (0.31), residues: 733 helix: 1.56 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.18 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.011 0.001 HIS D 82 PHE 0.010 0.001 PHE F 61 TYR 0.045 0.002 TYR D 83 ARG 0.010 0.000 ARG C 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 235 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8429 (mt-10) REVERT: A 74 ILE cc_start: 0.9508 (tt) cc_final: 0.9273 (tt) REVERT: A 78 PHE cc_start: 0.8895 (m-10) cc_final: 0.8597 (m-80) REVERT: A 87 GLN cc_start: 0.9361 (mt0) cc_final: 0.9151 (mt0) REVERT: A 95 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8805 (tt0) REVERT: A 104 HIS cc_start: 0.8426 (t-90) cc_final: 0.7922 (t70) REVERT: A 107 GLU cc_start: 0.8830 (pp20) cc_final: 0.8192 (pp20) REVERT: A 108 ASP cc_start: 0.8328 (m-30) cc_final: 0.7539 (m-30) REVERT: A 122 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8248 (m-80) REVERT: A 127 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8673 (tm-30) REVERT: B 79 LYS cc_start: 0.8965 (mtmm) cc_final: 0.8669 (ttmm) REVERT: B 84 MET cc_start: 0.8708 (tpp) cc_final: 0.8129 (tpp) REVERT: C 32 ARG cc_start: 0.9318 (ttp80) cc_final: 0.9069 (ptm-80) REVERT: C 39 TYR cc_start: 0.8742 (m-80) cc_final: 0.8493 (m-80) REVERT: C 56 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8343 (mm-30) REVERT: C 64 GLU cc_start: 0.8515 (tp30) cc_final: 0.8230 (tp30) REVERT: C 95 LYS cc_start: 0.9611 (ttmm) cc_final: 0.9194 (tptt) REVERT: C 104 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7917 (tp-100) REVERT: D 35 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7919 (mm-30) REVERT: D 37 TYR cc_start: 0.9492 (m-80) cc_final: 0.9286 (m-10) REVERT: D 42 TYR cc_start: 0.8303 (t80) cc_final: 0.8072 (t80) REVERT: D 47 GLN cc_start: 0.9357 (tm-30) cc_final: 0.8997 (tm-30) REVERT: D 71 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8509 (tm-30) REVERT: D 93 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8548 (mm-30) REVERT: D 95 GLN cc_start: 0.9239 (tt0) cc_final: 0.8978 (tm-30) REVERT: E 85 ASN cc_start: 0.8952 (m-40) cc_final: 0.8671 (m-40) REVERT: E 104 HIS cc_start: 0.9027 (t-90) cc_final: 0.8610 (t70) REVERT: E 130 ARG cc_start: 0.9629 (mtp180) cc_final: 0.9343 (ptm160) REVERT: F 52 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8436 (tp30) REVERT: F 84 MET cc_start: 0.8262 (tpp) cc_final: 0.7949 (tpp) REVERT: F 88 TYR cc_start: 0.8605 (m-10) cc_final: 0.8120 (m-80) REVERT: F 91 LYS cc_start: 0.9293 (ttpt) cc_final: 0.8989 (tptt) REVERT: G 36 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8636 (mmmt) REVERT: G 39 TYR cc_start: 0.8812 (m-80) cc_final: 0.8561 (m-80) REVERT: G 95 LYS cc_start: 0.8986 (ttpt) cc_final: 0.8623 (ttmm) REVERT: H 37 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.8018 (p90) REVERT: H 46 LYS cc_start: 0.9085 (tppt) cc_final: 0.8552 (tppt) REVERT: H 83 TYR cc_start: 0.8510 (m-10) cc_final: 0.8002 (m-10) REVERT: H 120 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8815 (tmtt) outliers start: 26 outliers final: 18 residues processed: 243 average time/residue: 0.3172 time to fit residues: 103.6185 Evaluate side-chains 245 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 223 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN D 82 HIS D 109 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.054216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.040513 restraints weight = 68418.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.041612 restraints weight = 35734.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.042426 restraints weight = 23995.374| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12730 Z= 0.312 Angle : 0.694 13.349 18433 Z= 0.395 Chirality : 0.038 0.215 2086 Planarity : 0.004 0.045 1322 Dihedral : 30.804 167.627 3997 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.34 % Allowed : 33.28 % Favored : 62.38 % 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: 1.05 (0.31), residues: 733 helix: 1.52 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.22 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 86 HIS 0.005 0.001 HIS F 75 PHE 0.011 0.002 PHE G 25 TYR 0.065 0.003 TYR D 83 ARG 0.010 0.001 ARG C 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2233.37 seconds wall clock time: 41 minutes 3.83 seconds (2463.83 seconds total)