Starting phenix.real_space_refine on Mon Nov 18 12:47:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynl_39426/11_2024/8ynl_39426.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynl_39426/11_2024/8ynl_39426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynl_39426/11_2024/8ynl_39426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynl_39426/11_2024/8ynl_39426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynl_39426/11_2024/8ynl_39426.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynl_39426/11_2024/8ynl_39426.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4446 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 8243 2.51 5 N 2226 2.21 5 O 2434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12977 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1510 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain: "B" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1510 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain: "C" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1510 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain: "H" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1403 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain breaks: 1 Chain: "I" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1386 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain breaks: 1 Chain: "J" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1386 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain breaks: 1 Chain: "K" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1424 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "G" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1424 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "F" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1424 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Time building chain proxies: 8.28, per 1000 atoms: 0.64 Number of scatterers: 12977 At special positions: 0 Unit cell: (104.16, 101.64, 146.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 2434 8.00 N 2226 7.00 C 8243 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.6 seconds 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3074 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 0 sheets defined 76.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.606A pdb=" N LEU A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 71 through 78 removed outlier: 4.106A pdb=" N LEU A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.585A pdb=" N MET A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 111 removed outlier: 3.552A pdb=" N VAL A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 111 " --> pdb=" O GLN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.848A pdb=" N ASP A 134 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 157 through 168 removed outlier: 4.124A pdb=" N GLN A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 182 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.767A pdb=" N LEU B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.617A pdb=" N ILE B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 79 removed outlier: 4.003A pdb=" N LEU B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.828A pdb=" N ASP B 134 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.578A pdb=" N ILE B 142 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 165 Processing helix chain 'B' and resid 169 through 182 Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.837A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU C 14 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.502A pdb=" N LEU C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 71 through 79 removed outlier: 3.736A pdb=" N LEU C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 157 through 165 Processing helix chain 'C' and resid 169 through 182 Processing helix chain 'H' and resid 3 through 12 removed outlier: 3.880A pdb=" N HIS H 7 " --> pdb=" O ALA H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 26 Processing helix chain 'H' and resid 36 through 47 Processing helix chain 'H' and resid 51 through 61 Processing helix chain 'H' and resid 64 through 71 Processing helix chain 'H' and resid 75 through 86 removed outlier: 3.551A pdb=" N VAL H 79 " --> pdb=" O ASP H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 102 Processing helix chain 'H' and resid 105 through 117 Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 149 through 159 Processing helix chain 'H' and resid 162 through 174 Processing helix chain 'I' and resid 2 through 13 removed outlier: 3.654A pdb=" N ILE I 6 " --> pdb=" O SER I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 25 Processing helix chain 'I' and resid 26 through 30 removed outlier: 3.867A pdb=" N ILE I 30 " --> pdb=" O ASP I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 47 Processing helix chain 'I' and resid 51 through 61 Processing helix chain 'I' and resid 64 through 71 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 91 through 102 removed outlier: 3.609A pdb=" N VAL I 95 " --> pdb=" O SER I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 117 Processing helix chain 'I' and resid 130 through 141 Processing helix chain 'I' and resid 149 through 159 Processing helix chain 'I' and resid 161 through 176 removed outlier: 3.859A pdb=" N LYS I 165 " --> pdb=" O ARG I 161 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN I 176 " --> pdb=" O LYS I 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 13 removed outlier: 3.641A pdb=" N ILE J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 26 Processing helix chain 'J' and resid 36 through 47 Processing helix chain 'J' and resid 51 through 62 Processing helix chain 'J' and resid 64 through 71 removed outlier: 3.743A pdb=" N LEU J 68 " --> pdb=" O ARG J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 91 through 103 removed outlier: 3.531A pdb=" N VAL J 95 " --> pdb=" O SER J 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 117 Processing helix chain 'J' and resid 130 through 141 Processing helix chain 'J' and resid 149 through 159 Processing helix chain 'J' and resid 161 through 175 removed outlier: 3.957A pdb=" N LYS J 165 " --> pdb=" O ARG J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 12 removed outlier: 3.724A pdb=" N ILE K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 25 removed outlier: 3.619A pdb=" N LYS K 18 " --> pdb=" O ASP K 14 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N MET K 20 " --> pdb=" O ASP K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 51 through 62 Processing helix chain 'K' and resid 64 through 71 Processing helix chain 'K' and resid 75 through 86 removed outlier: 3.631A pdb=" N VAL K 79 " --> pdb=" O ASP K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 102 removed outlier: 3.530A pdb=" N VAL K 95 " --> pdb=" O SER K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 116 removed outlier: 3.560A pdb=" N VAL K 109 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER K 110 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER K 111 " --> pdb=" O SER K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'K' and resid 149 through 159 Processing helix chain 'K' and resid 162 through 175 Processing helix chain 'G' and resid 2 through 12 removed outlier: 3.728A pdb=" N ILE G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 25 removed outlier: 3.663A pdb=" N GLU G 19 " --> pdb=" O THR G 15 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET G 20 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 47 Processing helix chain 'G' and resid 51 through 62 Processing helix chain 'G' and resid 64 through 71 Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 91 through 103 Processing helix chain 'G' and resid 105 through 116 removed outlier: 4.121A pdb=" N SER G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 141 Processing helix chain 'G' and resid 149 through 159 removed outlier: 3.516A pdb=" N ILE G 159 " --> pdb=" O CYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 175 removed outlier: 3.644A pdb=" N VAL G 175 " --> pdb=" O TYR G 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 removed outlier: 3.550A pdb=" N LEU F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 25 removed outlier: 3.591A pdb=" N LYS F 18 " --> pdb=" O ASP F 14 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU F 19 " --> pdb=" O THR F 15 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET F 20 " --> pdb=" O ASP F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 47 Processing helix chain 'F' and resid 51 through 62 removed outlier: 3.523A pdb=" N VAL F 62 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 71 Processing helix chain 'F' and resid 75 through 86 removed outlier: 3.524A pdb=" N VAL F 79 " --> pdb=" O ASP F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 104 Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.617A pdb=" N SER F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 141 Processing helix chain 'F' and resid 149 through 158 Processing helix chain 'F' and resid 161 through 175 removed outlier: 4.027A pdb=" N LYS F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) 724 hydrogen bonds defined for protein. 2151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4343 1.34 - 1.46: 2271 1.46 - 1.58: 6368 1.58 - 1.69: 0 1.69 - 1.81: 130 Bond restraints: 13112 Sorted by residual: bond pdb=" CA THR H 166 " pdb=" C THR H 166 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.26e-02 6.30e+03 4.00e+00 bond pdb=" C THR H 166 " pdb=" N LYS H 167 " ideal model delta sigma weight residual 1.335 1.323 0.011 1.25e-02 6.40e+03 8.11e-01 bond pdb=" CA PRO H 34 " pdb=" C PRO H 34 " ideal model delta sigma weight residual 1.517 1.511 0.006 6.70e-03 2.23e+04 6.76e-01 bond pdb=" C ILE B 151 " pdb=" N LEU B 152 " ideal model delta sigma weight residual 1.330 1.341 -0.011 1.36e-02 5.41e+03 6.26e-01 bond pdb=" CB PRO H 87 " pdb=" CG PRO H 87 " ideal model delta sigma weight residual 1.492 1.529 -0.037 5.00e-02 4.00e+02 5.41e-01 ... (remaining 13107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 17121 1.00 - 1.99: 352 1.99 - 2.99: 61 2.99 - 3.98: 24 3.98 - 4.98: 11 Bond angle restraints: 17569 Sorted by residual: angle pdb=" N THR H 166 " pdb=" CA THR H 166 " pdb=" C THR H 166 " ideal model delta sigma weight residual 111.14 106.35 4.79 1.08e+00 8.57e-01 1.97e+01 angle pdb=" N ILE A 69 " pdb=" CA ILE A 69 " pdb=" C ILE A 69 " ideal model delta sigma weight residual 112.29 108.98 3.31 9.40e-01 1.13e+00 1.24e+01 angle pdb=" N VAL J 62 " pdb=" CA VAL J 62 " pdb=" C VAL J 62 " ideal model delta sigma weight residual 112.98 108.68 4.30 1.25e+00 6.40e-01 1.18e+01 angle pdb=" CA THR H 166 " pdb=" CB THR H 166 " pdb=" OG1 THR H 166 " ideal model delta sigma weight residual 109.60 104.62 4.98 1.50e+00 4.44e-01 1.10e+01 angle pdb=" C LYS H 165 " pdb=" N THR H 166 " pdb=" CA THR H 166 " ideal model delta sigma weight residual 120.44 116.90 3.54 1.36e+00 5.41e-01 6.78e+00 ... (remaining 17564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 7451 17.54 - 35.08: 738 35.08 - 52.62: 107 52.62 - 70.16: 18 70.16 - 87.69: 15 Dihedral angle restraints: 8329 sinusoidal: 3642 harmonic: 4687 Sorted by residual: dihedral pdb=" CA ASP A 73 " pdb=" CB ASP A 73 " pdb=" CG ASP A 73 " pdb=" OD1 ASP A 73 " ideal model delta sinusoidal sigma weight residual -30.00 -86.67 56.67 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CB GLU B 12 " pdb=" CG GLU B 12 " pdb=" CD GLU B 12 " pdb=" OE1 GLU B 12 " ideal model delta sinusoidal sigma weight residual 0.00 -85.29 85.29 1 3.00e+01 1.11e-03 9.79e+00 dihedral pdb=" CB MET G 97 " pdb=" CG MET G 97 " pdb=" SD MET G 97 " pdb=" CE MET G 97 " ideal model delta sinusoidal sigma weight residual 180.00 120.91 59.09 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 8326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1432 0.028 - 0.056: 414 0.056 - 0.084: 149 0.084 - 0.113: 45 0.113 - 0.141: 10 Chirality restraints: 2050 Sorted by residual: chirality pdb=" CB VAL F 62 " pdb=" CA VAL F 62 " pdb=" CG1 VAL F 62 " pdb=" CG2 VAL F 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CB VAL A 150 " pdb=" CA VAL A 150 " pdb=" CG1 VAL A 150 " pdb=" CG2 VAL A 150 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CB VAL C 150 " pdb=" CA VAL C 150 " pdb=" CG1 VAL C 150 " pdb=" CG2 VAL C 150 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 2047 not shown) Planarity restraints: 2230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 165 " -0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C LYS H 165 " 0.023 2.00e-02 2.50e+03 pdb=" O LYS H 165 " -0.009 2.00e-02 2.50e+03 pdb=" N THR H 166 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 145 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO F 146 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO F 146 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 146 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 145 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO I 146 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO I 146 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO I 146 " 0.015 5.00e-02 4.00e+02 ... (remaining 2227 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3144 2.80 - 3.33: 12718 3.33 - 3.85: 19691 3.85 - 4.38: 21996 4.38 - 4.90: 38279 Nonbonded interactions: 95828 Sorted by model distance: nonbonded pdb=" OE1 GLU F 17 " pdb=" NH2 ARG F 64 " model vdw 2.280 3.120 nonbonded pdb=" O ASP K 163 " pdb=" OG1 THR K 166 " model vdw 2.282 3.040 nonbonded pdb=" OE1 GLU G 17 " pdb=" NH2 ARG G 64 " model vdw 2.296 3.120 nonbonded pdb=" OD1 ASP B 28 " pdb=" NH2 ARG B 102 " model vdw 2.308 3.120 nonbonded pdb=" O ASP G 163 " pdb=" OG1 THR G 166 " model vdw 2.320 3.040 ... (remaining 95823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'F' and (resid 2 through 28 or resid 31 through 121 or resid 128 through \ 175)) selection = (chain 'G' and (resid 2 through 28 or resid 31 through 121 or resid 128 through \ 175)) selection = (chain 'H' and (resid 2 through 121 or resid 128 through 175)) selection = (chain 'I' and (resid 2 through 28 or resid 31 through 175)) selection = (chain 'J' and (resid 2 through 28 or resid 31 through 121 or resid 128 through \ 175)) selection = (chain 'K' and (resid 2 through 28 or resid 31 through 121 or resid 128 through \ 175)) } 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 29.660 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.002 0.037 13112 Z= 0.107 Angle : 0.390 4.980 17569 Z= 0.221 Chirality : 0.033 0.141 2050 Planarity : 0.002 0.028 2230 Dihedral : 13.834 87.694 5255 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 1.87 (0.22), residues: 1559 helix: 1.94 (0.16), residues: 1171 sheet: None (None), residues: 0 loop : -0.96 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 160 PHE 0.011 0.001 PHE B 3 TYR 0.010 0.001 TYR C 101 ARG 0.001 0.000 ARG K 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.8322 (t80) cc_final: 0.8037 (t80) REVERT: B 172 LEU cc_start: 0.9114 (mp) cc_final: 0.8893 (mm) REVERT: C 1 MET cc_start: 0.6163 (ptt) cc_final: 0.5920 (ttt) REVERT: C 29 TYR cc_start: 0.8558 (m-80) cc_final: 0.8303 (m-80) REVERT: C 34 LYS cc_start: 0.8550 (mmtm) cc_final: 0.8289 (mttt) REVERT: C 46 GLN cc_start: 0.8480 (mt0) cc_final: 0.8268 (mt0) REVERT: C 95 ARG cc_start: 0.7532 (mmt90) cc_final: 0.6868 (tpp80) REVERT: C 101 TYR cc_start: 0.7802 (t80) cc_final: 0.7542 (t80) REVERT: C 124 LEU cc_start: 0.8208 (mt) cc_final: 0.7681 (pp) REVERT: C 163 VAL cc_start: 0.9215 (t) cc_final: 0.8761 (p) REVERT: C 181 PHE cc_start: 0.7862 (m-10) cc_final: 0.7308 (m-80) REVERT: H 41 LEU cc_start: 0.9397 (mm) cc_final: 0.9107 (mt) REVERT: I 6 ILE cc_start: 0.8891 (pt) cc_final: 0.8560 (mt) REVERT: I 86 ASN cc_start: 0.8545 (m-40) cc_final: 0.8070 (m110) REVERT: J 93 TYR cc_start: 0.8598 (t80) cc_final: 0.8297 (t80) REVERT: J 97 MET cc_start: 0.8806 (mmt) cc_final: 0.8468 (mmt) REVERT: K 74 MET cc_start: 0.7815 (mtp) cc_final: 0.7515 (ttm) REVERT: G 1 MET cc_start: 0.6529 (ttp) cc_final: 0.5969 (mpp) REVERT: G 133 ASP cc_start: 0.8192 (t0) cc_final: 0.7946 (t0) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.2616 time to fit residues: 136.4285 Evaluate side-chains 200 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 0.0980 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN B 176 ASN H 88 HIS I 86 ASN I 148 GLN G 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13112 Z= 0.184 Angle : 0.538 11.525 17569 Z= 0.279 Chirality : 0.037 0.140 2050 Planarity : 0.003 0.042 2230 Dihedral : 3.350 12.310 1731 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.76 % Allowed : 9.59 % Favored : 88.66 % 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: 1.69 (0.22), residues: 1559 helix: 1.69 (0.16), residues: 1199 sheet: None (None), residues: 0 loop : -0.77 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 160 PHE 0.017 0.001 PHE A 120 TYR 0.008 0.001 TYR H 119 ARG 0.007 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8668 (tt0) cc_final: 0.8264 (mm-40) REVERT: B 137 MET cc_start: 0.8270 (mtp) cc_final: 0.7929 (mtp) REVERT: C 1 MET cc_start: 0.6193 (ptt) cc_final: 0.5981 (ttt) REVERT: C 29 TYR cc_start: 0.8563 (m-80) cc_final: 0.8297 (m-80) REVERT: C 95 ARG cc_start: 0.7376 (mmt90) cc_final: 0.7003 (mmt90) REVERT: C 101 TYR cc_start: 0.7924 (t80) cc_final: 0.7630 (t80) REVERT: C 124 LEU cc_start: 0.8242 (mt) cc_final: 0.7772 (pp) REVERT: C 163 VAL cc_start: 0.9211 (t) cc_final: 0.8934 (p) REVERT: H 44 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8597 (mm) REVERT: H 82 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.8098 (m-70) REVERT: I 85 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7628 (ttp-110) REVERT: I 86 ASN cc_start: 0.8647 (m110) cc_final: 0.8295 (m-40) REVERT: J 1 MET cc_start: 0.7013 (ttm) cc_final: 0.6688 (ttp) REVERT: J 11 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: J 93 TYR cc_start: 0.8604 (t80) cc_final: 0.8230 (t80) REVERT: K 31 ASP cc_start: 0.7138 (p0) cc_final: 0.6929 (p0) REVERT: K 74 MET cc_start: 0.7773 (mtp) cc_final: 0.7525 (ttm) REVERT: G 75 ASP cc_start: 0.7535 (p0) cc_final: 0.7187 (p0) REVERT: G 116 MET cc_start: 0.8578 (mmm) cc_final: 0.8104 (mmm) REVERT: G 133 ASP cc_start: 0.8430 (t0) cc_final: 0.8013 (t0) REVERT: F 17 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8062 (mt-10) outliers start: 26 outliers final: 15 residues processed: 224 average time/residue: 0.2344 time to fit residues: 77.4933 Evaluate side-chains 203 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 11 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 118 ASP Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain F residue 166 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.0370 chunk 43 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 140 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 overall best weight: 3.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 HIS G 8 GLN G 86 ASN F 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13112 Z= 0.390 Angle : 0.655 7.209 17569 Z= 0.331 Chirality : 0.041 0.154 2050 Planarity : 0.004 0.054 2230 Dihedral : 3.729 15.917 1731 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.23 % Allowed : 12.69 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.22), residues: 1559 helix: 1.45 (0.16), residues: 1193 sheet: None (None), residues: 0 loop : -0.90 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS I 160 PHE 0.014 0.002 PHE A 61 TYR 0.014 0.002 TYR A 106 ARG 0.007 0.001 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8143 (tm-30) REVERT: A 46 GLN cc_start: 0.8781 (tt0) cc_final: 0.8507 (tp40) REVERT: C 95 ARG cc_start: 0.7501 (mmt90) cc_final: 0.7086 (mmt90) REVERT: C 101 TYR cc_start: 0.8223 (t80) cc_final: 0.7721 (t80) REVERT: C 124 LEU cc_start: 0.8137 (mt) cc_final: 0.7682 (pp) REVERT: H 82 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.8147 (m-70) REVERT: I 85 ARG cc_start: 0.7972 (ttp-110) cc_final: 0.7650 (ttp-110) REVERT: I 86 ASN cc_start: 0.8610 (m110) cc_final: 0.8039 (m110) REVERT: J 1 MET cc_start: 0.7133 (ttm) cc_final: 0.6839 (ttp) REVERT: J 130 SER cc_start: 0.8915 (t) cc_final: 0.8692 (p) REVERT: K 31 ASP cc_start: 0.7129 (p0) cc_final: 0.6871 (p0) REVERT: K 74 MET cc_start: 0.7918 (mtp) cc_final: 0.7523 (ttm) REVERT: G 8 GLN cc_start: 0.8715 (mm110) cc_final: 0.8502 (mm-40) REVERT: G 116 MET cc_start: 0.8656 (mmm) cc_final: 0.7978 (mmt) outliers start: 33 outliers final: 23 residues processed: 208 average time/residue: 0.2224 time to fit residues: 70.3919 Evaluate side-chains 198 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 118 ASP Chi-restraints excluded: chain J residue 169 GLN Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain F residue 166 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 142 optimal weight: 0.4980 chunk 150 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 ASN H 88 HIS ** K 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13112 Z= 0.157 Angle : 0.515 10.641 17569 Z= 0.264 Chirality : 0.036 0.152 2050 Planarity : 0.003 0.058 2230 Dihedral : 3.600 17.224 1731 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.96 % Allowed : 14.45 % Favored : 83.59 % 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: 1.53 (0.22), residues: 1559 helix: 1.58 (0.16), residues: 1198 sheet: None (None), residues: 0 loop : -0.84 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS G 7 PHE 0.017 0.001 PHE A 181 TYR 0.008 0.001 TYR B 106 ARG 0.014 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8180 (tm-30) REVERT: A 46 GLN cc_start: 0.8698 (tt0) cc_final: 0.8431 (tp40) REVERT: A 124 LEU cc_start: 0.9091 (tp) cc_final: 0.8709 (tt) REVERT: B 80 ASN cc_start: 0.9024 (t0) cc_final: 0.8810 (t0) REVERT: C 46 GLN cc_start: 0.8316 (mt0) cc_final: 0.8064 (mm-40) REVERT: C 95 ARG cc_start: 0.7567 (mmt90) cc_final: 0.7142 (mmt90) REVERT: C 101 TYR cc_start: 0.8095 (t80) cc_final: 0.7647 (t80) REVERT: C 124 LEU cc_start: 0.8240 (mt) cc_final: 0.7834 (pp) REVERT: H 82 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.8080 (m-70) REVERT: H 129 LYS cc_start: 0.8307 (ptmt) cc_final: 0.8023 (mmmt) REVERT: I 85 ARG cc_start: 0.7932 (ttp-110) cc_final: 0.7627 (ttp-110) REVERT: I 86 ASN cc_start: 0.8642 (m110) cc_final: 0.8079 (m110) REVERT: I 120 MET cc_start: 0.7646 (ptm) cc_final: 0.7292 (ptm) REVERT: J 1 MET cc_start: 0.6977 (ttm) cc_final: 0.6738 (ttp) REVERT: J 83 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8236 (mt) REVERT: K 74 MET cc_start: 0.7850 (mtp) cc_final: 0.7514 (ttm) REVERT: G 1 MET cc_start: 0.7158 (mpp) cc_final: 0.6844 (mmp) REVERT: G 8 GLN cc_start: 0.8716 (mm110) cc_final: 0.8444 (mm-40) REVERT: G 116 MET cc_start: 0.8786 (mmm) cc_final: 0.7624 (mmt) REVERT: F 64 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7075 (tpp-160) REVERT: F 116 MET cc_start: 0.7777 (mmm) cc_final: 0.7557 (mmt) outliers start: 29 outliers final: 19 residues processed: 213 average time/residue: 0.2328 time to fit residues: 74.1476 Evaluate side-chains 201 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 118 ASP Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 64 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 HIS ** K 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13112 Z= 0.154 Angle : 0.494 8.443 17569 Z= 0.257 Chirality : 0.036 0.259 2050 Planarity : 0.003 0.030 2230 Dihedral : 3.494 14.305 1731 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.69 % Allowed : 16.07 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1559 helix: 1.61 (0.16), residues: 1199 sheet: None (None), residues: 0 loop : -0.80 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 7 PHE 0.010 0.001 PHE B 120 TYR 0.011 0.001 TYR A 101 ARG 0.007 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8695 (tt0) cc_final: 0.8415 (tp40) REVERT: A 124 LEU cc_start: 0.9097 (tp) cc_final: 0.8845 (tt) REVERT: C 46 GLN cc_start: 0.8270 (mt0) cc_final: 0.8035 (mm-40) REVERT: C 95 ARG cc_start: 0.7565 (mmt90) cc_final: 0.7104 (mmt90) REVERT: C 101 TYR cc_start: 0.7909 (t80) cc_final: 0.7633 (t80) REVERT: C 124 LEU cc_start: 0.8164 (mt) cc_final: 0.7868 (pp) REVERT: H 82 HIS cc_start: 0.8384 (OUTLIER) cc_final: 0.8073 (m-70) REVERT: I 85 ARG cc_start: 0.7912 (ttp-110) cc_final: 0.7699 (ttp-110) REVERT: I 86 ASN cc_start: 0.8641 (m110) cc_final: 0.8120 (m110) REVERT: I 120 MET cc_start: 0.7608 (ptm) cc_final: 0.7264 (ptm) REVERT: J 1 MET cc_start: 0.6977 (ttm) cc_final: 0.6756 (ttp) REVERT: J 83 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8192 (mt) REVERT: J 93 TYR cc_start: 0.8505 (t80) cc_final: 0.8083 (t80) REVERT: K 74 MET cc_start: 0.7822 (mtp) cc_final: 0.7557 (ttm) REVERT: K 116 MET cc_start: 0.8166 (mtm) cc_final: 0.7801 (mtm) REVERT: G 1 MET cc_start: 0.7166 (mpp) cc_final: 0.6591 (mmp) REVERT: G 8 GLN cc_start: 0.8810 (mm110) cc_final: 0.8521 (mm-40) REVERT: G 116 MET cc_start: 0.8683 (mmm) cc_final: 0.8402 (mmp) REVERT: F 97 MET cc_start: 0.8445 (mmm) cc_final: 0.8056 (mmm) outliers start: 25 outliers final: 18 residues processed: 212 average time/residue: 0.2292 time to fit residues: 72.8303 Evaluate side-chains 196 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 118 ASP Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain F residue 15 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 HIS ** K 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13112 Z= 0.158 Angle : 0.513 7.867 17569 Z= 0.264 Chirality : 0.036 0.166 2050 Planarity : 0.003 0.065 2230 Dihedral : 3.491 16.426 1731 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.89 % Allowed : 16.68 % Favored : 81.43 % 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: 1.58 (0.22), residues: 1559 helix: 1.60 (0.16), residues: 1199 sheet: None (None), residues: 0 loop : -0.78 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 7 PHE 0.019 0.001 PHE A 181 TYR 0.011 0.001 TYR K 93 ARG 0.015 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8692 (tt0) cc_final: 0.8404 (tp40) REVERT: A 124 LEU cc_start: 0.9147 (tp) cc_final: 0.8818 (tt) REVERT: C 46 GLN cc_start: 0.8285 (mt0) cc_final: 0.8067 (mm-40) REVERT: C 95 ARG cc_start: 0.7602 (mmt90) cc_final: 0.7110 (mmt90) REVERT: C 101 TYR cc_start: 0.7940 (t80) cc_final: 0.7624 (t80) REVERT: C 124 LEU cc_start: 0.8049 (mt) cc_final: 0.7620 (pp) REVERT: H 82 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.8056 (m-70) REVERT: I 85 ARG cc_start: 0.7928 (ttp-110) cc_final: 0.7726 (ttp-110) REVERT: I 86 ASN cc_start: 0.8652 (m110) cc_final: 0.8315 (m110) REVERT: I 120 MET cc_start: 0.7634 (ptm) cc_final: 0.7298 (ptm) REVERT: J 93 TYR cc_start: 0.8492 (t80) cc_final: 0.8040 (t80) REVERT: J 132 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8329 (mm) REVERT: K 74 MET cc_start: 0.7820 (mtp) cc_final: 0.7578 (ttm) REVERT: K 116 MET cc_start: 0.8135 (mtm) cc_final: 0.7787 (mtm) REVERT: G 1 MET cc_start: 0.7069 (mpp) cc_final: 0.6499 (mmp) REVERT: G 8 GLN cc_start: 0.8868 (mm110) cc_final: 0.8566 (mm-40) REVERT: G 116 MET cc_start: 0.8644 (mmm) cc_final: 0.8427 (mmp) REVERT: F 97 MET cc_start: 0.8427 (mmm) cc_final: 0.8070 (mmm) outliers start: 28 outliers final: 21 residues processed: 202 average time/residue: 0.2214 time to fit residues: 68.0363 Evaluate side-chains 199 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 118 ASP Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain F residue 15 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 GLN H 88 HIS ** K 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13112 Z= 0.152 Angle : 0.502 8.402 17569 Z= 0.260 Chirality : 0.036 0.243 2050 Planarity : 0.003 0.053 2230 Dihedral : 3.480 17.917 1731 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.28 % Allowed : 17.42 % Favored : 81.30 % 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: 1.61 (0.22), residues: 1559 helix: 1.61 (0.16), residues: 1199 sheet: None (None), residues: 0 loop : -0.72 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 160 PHE 0.010 0.001 PHE B 120 TYR 0.009 0.001 TYR C 101 ARG 0.013 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8080 (tm-30) REVERT: A 46 GLN cc_start: 0.8692 (tt0) cc_final: 0.8281 (tp40) REVERT: A 124 LEU cc_start: 0.9089 (tp) cc_final: 0.8887 (tp) REVERT: A 134 ASP cc_start: 0.9147 (t70) cc_final: 0.8751 (t70) REVERT: C 95 ARG cc_start: 0.7531 (mmt90) cc_final: 0.6994 (mmt90) REVERT: C 101 TYR cc_start: 0.7958 (t80) cc_final: 0.7667 (t80) REVERT: C 124 LEU cc_start: 0.8081 (mt) cc_final: 0.7852 (pp) REVERT: C 146 MET cc_start: 0.8575 (mtm) cc_final: 0.8061 (mtm) REVERT: H 82 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.8092 (m-70) REVERT: I 85 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7715 (ttp-110) REVERT: I 86 ASN cc_start: 0.8612 (m110) cc_final: 0.8286 (m110) REVERT: J 83 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8156 (pp) REVERT: J 93 TYR cc_start: 0.8512 (t80) cc_final: 0.8031 (t80) REVERT: J 132 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8343 (mm) REVERT: K 74 MET cc_start: 0.7806 (mtp) cc_final: 0.7572 (ttm) REVERT: K 116 MET cc_start: 0.8098 (mtm) cc_final: 0.7745 (mtm) REVERT: G 8 GLN cc_start: 0.8857 (mm110) cc_final: 0.8581 (mm-40) REVERT: F 97 MET cc_start: 0.8424 (mmm) cc_final: 0.8091 (mmm) outliers start: 19 outliers final: 16 residues processed: 197 average time/residue: 0.2202 time to fit residues: 65.8782 Evaluate side-chains 194 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 118 ASP Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain F residue 15 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 0.0870 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 GLN H 88 HIS ** K 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13112 Z= 0.136 Angle : 0.506 9.844 17569 Z= 0.260 Chirality : 0.036 0.219 2050 Planarity : 0.003 0.038 2230 Dihedral : 3.418 17.946 1731 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.62 % Allowed : 17.29 % Favored : 81.09 % 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: 1.63 (0.22), residues: 1559 helix: 1.63 (0.16), residues: 1199 sheet: None (None), residues: 0 loop : -0.71 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 7 PHE 0.021 0.001 PHE A 181 TYR 0.016 0.001 TYR G 93 ARG 0.005 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8086 (tm-30) REVERT: A 46 GLN cc_start: 0.8675 (tt0) cc_final: 0.8274 (tp40) REVERT: A 134 ASP cc_start: 0.9157 (t70) cc_final: 0.8815 (t70) REVERT: B 137 MET cc_start: 0.8090 (ptm) cc_final: 0.7742 (ptp) REVERT: C 95 ARG cc_start: 0.7611 (mmt90) cc_final: 0.7053 (mmt90) REVERT: C 101 TYR cc_start: 0.7884 (t80) cc_final: 0.7571 (t80) REVERT: C 124 LEU cc_start: 0.7969 (mt) cc_final: 0.7656 (pp) REVERT: H 82 HIS cc_start: 0.8414 (OUTLIER) cc_final: 0.8147 (m-70) REVERT: J 83 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8131 (pp) REVERT: J 93 TYR cc_start: 0.8485 (t80) cc_final: 0.8009 (t80) REVERT: J 132 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8324 (mm) REVERT: K 39 ASP cc_start: 0.8064 (m-30) cc_final: 0.7839 (t0) REVERT: K 116 MET cc_start: 0.7879 (mtm) cc_final: 0.7616 (mtm) REVERT: G 8 GLN cc_start: 0.8878 (mm110) cc_final: 0.8600 (mm-40) REVERT: F 97 MET cc_start: 0.8411 (mmm) cc_final: 0.8050 (mmm) outliers start: 24 outliers final: 15 residues processed: 202 average time/residue: 0.2336 time to fit residues: 70.6653 Evaluate side-chains 199 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 144 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 139 optimal weight: 0.2980 chunk 92 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 GLN H 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13112 Z= 0.142 Angle : 0.520 10.473 17569 Z= 0.266 Chirality : 0.036 0.209 2050 Planarity : 0.002 0.032 2230 Dihedral : 3.384 18.281 1731 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.62 % Allowed : 17.69 % Favored : 80.69 % 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: 1.67 (0.22), residues: 1559 helix: 1.61 (0.16), residues: 1200 sheet: None (None), residues: 0 loop : -0.53 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 82 PHE 0.021 0.001 PHE C 143 TYR 0.014 0.001 TYR G 93 ARG 0.004 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8080 (tm-30) REVERT: A 46 GLN cc_start: 0.8670 (tt0) cc_final: 0.8273 (tp40) REVERT: A 134 ASP cc_start: 0.9157 (t70) cc_final: 0.8857 (t0) REVERT: B 137 MET cc_start: 0.8011 (ptm) cc_final: 0.7670 (ptp) REVERT: C 95 ARG cc_start: 0.7600 (mmt90) cc_final: 0.7033 (mmt90) REVERT: C 101 TYR cc_start: 0.7878 (t80) cc_final: 0.7569 (t80) REVERT: H 82 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.8150 (m-70) REVERT: J 83 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8142 (pp) REVERT: J 93 TYR cc_start: 0.8495 (t80) cc_final: 0.8079 (t80) REVERT: J 132 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8348 (mm) REVERT: K 39 ASP cc_start: 0.8061 (m-30) cc_final: 0.7836 (t0) REVERT: K 116 MET cc_start: 0.7920 (mtm) cc_final: 0.7524 (mtm) REVERT: G 8 GLN cc_start: 0.8885 (mm110) cc_final: 0.8608 (mm-40) REVERT: G 11 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7421 (mt-10) outliers start: 24 outliers final: 18 residues processed: 205 average time/residue: 0.2289 time to fit residues: 71.1236 Evaluate side-chains 203 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 0.0570 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 80 ASN C 35 GLN H 88 HIS F 173 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13112 Z= 0.146 Angle : 0.535 10.644 17569 Z= 0.272 Chirality : 0.036 0.223 2050 Planarity : 0.003 0.033 2230 Dihedral : 3.386 19.641 1731 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.69 % Allowed : 18.16 % Favored : 80.15 % 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: 1.63 (0.22), residues: 1559 helix: 1.59 (0.16), residues: 1206 sheet: None (None), residues: 0 loop : -0.61 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 7 PHE 0.023 0.001 PHE C 143 TYR 0.014 0.001 TYR G 93 ARG 0.007 0.000 ARG I 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8087 (tm-30) REVERT: A 46 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8299 (tp40) REVERT: A 134 ASP cc_start: 0.9149 (t70) cc_final: 0.8764 (t0) REVERT: A 137 MET cc_start: 0.5321 (mmt) cc_final: 0.5101 (mmt) REVERT: B 137 MET cc_start: 0.7943 (ptm) cc_final: 0.7646 (ptp) REVERT: C 95 ARG cc_start: 0.7603 (mmt90) cc_final: 0.7025 (mmt90) REVERT: C 101 TYR cc_start: 0.7891 (t80) cc_final: 0.7571 (t80) REVERT: H 82 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.8158 (m-70) REVERT: J 83 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8138 (pp) REVERT: J 132 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8353 (mm) REVERT: K 39 ASP cc_start: 0.8065 (m-30) cc_final: 0.7847 (t0) REVERT: K 116 MET cc_start: 0.7979 (mtm) cc_final: 0.7697 (mtm) REVERT: G 8 GLN cc_start: 0.8874 (mm110) cc_final: 0.8584 (mm-40) REVERT: G 11 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7364 (mt-10) outliers start: 25 outliers final: 17 residues processed: 201 average time/residue: 0.2232 time to fit residues: 68.0137 Evaluate side-chains 196 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain F residue 15 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 0.0170 chunk 123 optimal weight: 9.9990 chunk 51 optimal weight: 0.0570 chunk 127 optimal weight: 0.0570 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 GLN H 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.100025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.077111 restraints weight = 33249.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.079983 restraints weight = 18075.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.081931 restraints weight = 12161.012| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13112 Z= 0.138 Angle : 0.535 10.602 17569 Z= 0.275 Chirality : 0.036 0.202 2050 Planarity : 0.003 0.034 2230 Dihedral : 3.363 20.175 1731 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.35 % Allowed : 18.97 % Favored : 79.68 % 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: 1.68 (0.22), residues: 1559 helix: 1.61 (0.16), residues: 1203 sheet: None (None), residues: 0 loop : -0.48 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 7 PHE 0.031 0.001 PHE C 143 TYR 0.013 0.001 TYR G 93 ARG 0.009 0.000 ARG I 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2537.50 seconds wall clock time: 47 minutes 27.35 seconds (2847.35 seconds total)