Starting phenix.real_space_refine on Tue Dec 31 02:01:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oh9_12897/12_2024/7oh9_12897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oh9_12897/12_2024/7oh9_12897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oh9_12897/12_2024/7oh9_12897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oh9_12897/12_2024/7oh9_12897.map" model { file = "/net/cci-nas-00/data/ceres_data/7oh9_12897/12_2024/7oh9_12897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oh9_12897/12_2024/7oh9_12897.cif" } resolution = 3.0 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 290 5.49 5 S 25 5.16 5 C 8612 2.51 5 N 2782 2.21 5 O 3390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15099 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1439 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Conformer: "B" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} bond proxies already assigned to first conformer: 1417 Chain: "L" Number of atoms: 823 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 96, 796 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'TRANS': 95} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 96, 796 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'TRANS': 95} Chain breaks: 2 bond proxies already assigned to first conformer: 775 Chain: "M" Number of atoms: 815 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 104, 807 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 104, 807 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 805 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N ALEU K 134 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU K 134 " occ=0.50 residue: pdb=" N ALYS K 138 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS K 138 " occ=0.50 residue: pdb=" N ASER K 184 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER K 184 " occ=0.50 residue: pdb=" N AGLU L 11 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU L 11 " occ=0.50 residue: pdb=" N AGLN L 280 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN L 280 " occ=0.50 residue: pdb=" N AGLU L 282 " occ=0.60 ... (16 atoms not shown) pdb=" OE2BGLU L 282 " occ=0.40 residue: pdb=" N AILE M 79 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE M 79 " occ=0.50 Time building chain proxies: 10.55, per 1000 atoms: 0.70 Number of scatterers: 15099 At special positions: 0 Unit cell: (93.45, 129.15, 142.8, 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 25 16.00 P 290 15.00 O 3390 8.00 N 2782 7.00 C 8612 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: 3.70 Conformation dependent library (CDL) restraints added in 1.7 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 60.5% alpha, 13.3% beta 143 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 7.09 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.022A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.502A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.380A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.614A 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 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.883A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.566A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.701A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.269A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 Processing helix chain 'K' and resid 81 through 89 removed outlier: 4.191A pdb=" N VAL K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 147 Processing helix chain 'K' and resid 171 through 179 Processing helix chain 'K' and resid 219 through 236 removed outlier: 3.615A pdb=" N ILE K 223 " --> pdb=" O GLN K 219 " (cutoff:3.500A) Proline residue: K 232 - end of helix Processing helix chain 'L' and resid 4 through 19 Processing helix chain 'L' and resid 20 through 27 removed outlier: 4.665A pdb=" N ASP L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 47 Processing helix chain 'M' and resid 8 through 12 removed outlier: 4.298A pdb=" N ARG M 11 " --> pdb=" O GLU M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 29 Processing helix chain 'M' and resid 33 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.092A pdb=" N ARG A 83 " --> 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 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.463A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.072A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.999A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.235A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 93 through 95 removed outlier: 6.189A pdb=" N GLU K 93 " --> pdb=" O ALA K 101 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ALA K 101 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN K 95 " --> pdb=" O PHE K 99 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR K 111 " --> pdb=" O ILE K 106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL K 122 " --> pdb=" O LEU K 114 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE K 70 " --> pdb=" O GLY K 125 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL K 161 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE K 70 " --> pdb=" O ASN K 159 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN K 159 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA K 72 " --> pdb=" O ILE K 157 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE K 157 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL K 74 " --> pdb=" O PHE K 155 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE K 155 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 243 through 253 removed outlier: 7.512A pdb=" N LEU L 243 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL L 267 " --> pdb=" O LEU L 243 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU L 245 " --> pdb=" O GLY L 265 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY L 265 " --> pdb=" O LEU L 245 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER L 261 " --> pdb=" O ASP L 249 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL L 251 " --> pdb=" O LYS L 259 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS L 259 " --> pdb=" O VAL L 251 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP L 264 " --> pdb=" O GLN L 277 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLN L 277 " --> pdb=" O ASP L 264 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL L 266 " --> pdb=" O THR L 275 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR L 275 " --> pdb=" O VAL L 266 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU M 60 " --> pdb=" O PHE L 276 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS L 278 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL M 62 " --> pdb=" O LYS L 278 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N AGLN L 280 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY M 64 " --> pdb=" O AGLN L 280 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N AGLU L 282 " --> pdb=" O GLY M 64 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU M 66 " --> pdb=" O AGLU L 282 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LYS M 59 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL M 87 " --> pdb=" O LYS M 59 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR M 61 " --> pdb=" O VAL M 85 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL M 85 " --> pdb=" O THR M 61 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS M 63 " --> pdb=" O CYS M 83 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N CYS M 83 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N AILE M 79 " --> pdb=" O ASP M 67 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR M 69 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR M 77 " --> pdb=" O TYR M 69 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE M 71 " --> pdb=" O VAL M 75 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL M 75 " --> pdb=" O PHE M 71 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL M 75 " --> pdb=" O CYS M 116 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N CYS M 116 " --> pdb=" O VAL M 75 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR M 77 " --> pdb=" O VAL M 114 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL M 114 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N AILE M 79 " --> pdb=" O ARG M 112 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG M 112 " --> pdb=" O AILE M 79 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS M 81 " --> pdb=" O LYS M 110 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LYS M 110 " --> pdb=" O LYS M 81 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS M 116 " --> pdb=" O CYS L 246 " (cutoff:3.500A) 566 hydrogen bonds defined for protein. 1669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 365 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 7.56 Time building geometry restraints manager: 4.34 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: 2919 1.33 - 1.45: 4821 1.45 - 1.57: 7592 1.57 - 1.69: 579 1.69 - 1.81: 41 Bond restraints: 15952 Sorted by residual: bond pdb=" CB PRO A 38 " pdb=" CG PRO A 38 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.65e+00 bond pdb=" CD GLU L 20 " pdb=" OE1 GLU L 20 " ideal model delta sigma weight residual 1.249 1.211 0.038 1.90e-02 2.77e+03 3.92e+00 bond pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.74e+00 bond pdb=" CB ASN M 55 " pdb=" CG ASN M 55 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.72e+00 bond pdb=" CG1 ILE D 58 " pdb=" CD1 ILE D 58 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.89e+00 ... (remaining 15947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 22510 2.73 - 5.45: 230 5.45 - 8.18: 36 8.18 - 10.90: 10 10.90 - 13.63: 2 Bond angle restraints: 22788 Sorted by residual: angle pdb=" N GLU L 20 " pdb=" CA GLU L 20 " pdb=" CB GLU L 20 " ideal model delta sigma weight residual 110.53 118.18 -7.65 1.47e+00 4.63e-01 2.71e+01 angle pdb=" C ASN L 19 " pdb=" N GLU L 20 " pdb=" CA GLU L 20 " ideal model delta sigma weight residual 121.92 113.28 8.64 1.73e+00 3.34e-01 2.50e+01 angle pdb=" CA GLU C 64 " pdb=" CB GLU C 64 " pdb=" CG GLU C 64 " ideal model delta sigma weight residual 114.10 123.46 -9.36 2.00e+00 2.50e-01 2.19e+01 angle pdb=" CA GLU L 20 " pdb=" CB GLU L 20 " pdb=" CG GLU L 20 " ideal model delta sigma weight residual 114.10 123.04 -8.94 2.00e+00 2.50e-01 2.00e+01 angle pdb=" C CYS M 72 " pdb=" N ASP M 73 " pdb=" CA ASP M 73 " ideal model delta sigma weight residual 121.54 129.97 -8.43 1.91e+00 2.74e-01 1.95e+01 ... (remaining 22783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.02: 6335 19.02 - 38.04: 1221 38.04 - 57.06: 1180 57.06 - 76.08: 152 76.08 - 95.10: 11 Dihedral angle restraints: 8899 sinusoidal: 5541 harmonic: 3358 Sorted by residual: dihedral pdb=" CA ASN L 19 " pdb=" C ASN L 19 " pdb=" N GLU L 20 " pdb=" CA GLU L 20 " ideal model delta harmonic sigma weight residual 180.00 145.51 34.49 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA GLU K 186 " pdb=" C GLU K 186 " pdb=" N PRO K 187 " pdb=" CA PRO K 187 " ideal model delta harmonic sigma weight residual -180.00 -146.31 -33.69 0 5.00e+00 4.00e-02 4.54e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -152.56 -27.44 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 8896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2256 0.069 - 0.139: 314 0.139 - 0.208: 29 0.208 - 0.277: 3 0.277 - 0.347: 4 Chirality restraints: 2606 Sorted by residual: chirality pdb=" CG LEU L 262 " pdb=" CB LEU L 262 " pdb=" CD1 LEU L 262 " pdb=" CD2 LEU L 262 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CG LEU M 19 " pdb=" CB LEU M 19 " pdb=" CD1 LEU M 19 " pdb=" CD2 LEU M 19 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CG LEU A 61 " pdb=" CB LEU A 61 " pdb=" CD1 LEU A 61 " pdb=" CD2 LEU A 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2603 not shown) Planarity restraints: 1879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN M 55 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ASN M 55 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN M 55 " 0.021 2.00e-02 2.50e+03 pdb=" N THR M 56 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 64 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" CD GLU C 64 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU C 64 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 64 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.02e+00 pdb=" N PRO C 80 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.034 5.00e-02 4.00e+02 ... (remaining 1876 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2547 2.77 - 3.30: 13473 3.30 - 3.83: 30580 3.83 - 4.37: 35913 4.37 - 4.90: 51531 Nonbonded interactions: 134044 Sorted by model distance: nonbonded pdb=" O ASP M 21 " pdb=" OG1 THR M 25 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR M 7 " pdb=" OD1 ASN M 117 " model vdw 2.250 3.040 nonbonded pdb=" OE1 GLU L 32 " pdb=" NE2 GLN L 36 " model vdw 2.293 3.120 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.294 3.040 nonbonded pdb=" O ALA L 4 " pdb=" OG SER L 7 " model vdw 2.295 3.040 ... (remaining 134039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 122) 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 44.130 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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 0.108 15952 Z= 0.391 Angle : 0.837 13.630 22788 Z= 0.468 Chirality : 0.050 0.347 2606 Planarity : 0.006 0.066 1879 Dihedral : 25.973 95.104 6729 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: -0.54 (0.23), residues: 1136 helix: 0.08 (0.18), residues: 678 sheet: 0.18 (0.49), residues: 120 loop : -1.25 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP M 76 HIS 0.007 0.001 HIS B 75 PHE 0.031 0.002 PHE M 78 TYR 0.038 0.003 TYR G 57 ARG 0.009 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 LYS cc_start: 0.8631 (tptm) cc_final: 0.8424 (mmmt) REVERT: D 68 GLU cc_start: 0.7644 (tp30) cc_final: 0.7443 (tp30) REVERT: D 90 GLU cc_start: 0.8280 (mp0) cc_final: 0.8027 (mp0) REVERT: F 59 LYS cc_start: 0.8707 (tttm) cc_final: 0.8500 (ttpp) REVERT: H 53 SER cc_start: 0.9119 (p) cc_final: 0.8740 (p) REVERT: H 65 ASP cc_start: 0.8494 (t70) cc_final: 0.8242 (t0) REVERT: K 88 HIS cc_start: 0.9195 (m-70) cc_final: 0.8874 (m-70) REVERT: K 104 MET cc_start: 0.8851 (pmm) cc_final: 0.8533 (ppp) REVERT: K 139 TYR cc_start: 0.8699 (m-80) cc_final: 0.8089 (m-10) REVERT: K 212 ILE cc_start: 0.9074 (mm) cc_final: 0.8829 (pp) REVERT: K 221 GLU cc_start: 0.8992 (tp30) cc_final: 0.8325 (tp30) REVERT: K 222 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8264 (mt-10) REVERT: K 224 TYR cc_start: 0.9266 (m-10) cc_final: 0.8985 (m-10) REVERT: K 225 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8705 (mm110) REVERT: L 248 TYR cc_start: 0.9024 (p90) cc_final: 0.8321 (p90) REVERT: M 78 PHE cc_start: 0.9298 (m-80) cc_final: 0.8918 (m-80) outliers start: 0 outliers final: 1 residues processed: 300 average time/residue: 1.6486 time to fit residues: 534.6388 Evaluate side-chains 260 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 30.0000 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 73 ASN C 104 GLN C 112 GLN D 92 GLN G 94 ASN H 44 GLN K 158 GLN ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15952 Z= 0.224 Angle : 0.651 11.635 22788 Z= 0.368 Chirality : 0.039 0.254 2606 Planarity : 0.004 0.053 1879 Dihedral : 29.466 105.574 4458 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.95 % Allowed : 15.06 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.59 (0.24), residues: 1136 helix: 1.14 (0.19), residues: 692 sheet: 0.36 (0.49), residues: 121 loop : -1.16 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 258 HIS 0.004 0.001 HIS B 75 PHE 0.027 0.001 PHE M 44 TYR 0.050 0.002 TYR L 10 ARG 0.007 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 282 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 90 GLU cc_start: 0.8461 (mp0) cc_final: 0.8184 (mp0) REVERT: E 120 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8309 (mtm) REVERT: H 65 ASP cc_start: 0.8521 (t70) cc_final: 0.8215 (t0) REVERT: K 88 HIS cc_start: 0.9230 (m-70) cc_final: 0.8755 (m-70) REVERT: K 91 ASN cc_start: 0.8995 (m-40) cc_final: 0.8515 (m-40) REVERT: K 93 GLU cc_start: 0.7352 (mp0) cc_final: 0.7124 (mp0) REVERT: K 121 MET cc_start: 0.8734 (ppp) cc_final: 0.8461 (ppp) REVERT: K 139 TYR cc_start: 0.8440 (m-80) cc_final: 0.7157 (m-80) REVERT: K 144 GLN cc_start: 0.8825 (mt0) cc_final: 0.8615 (mm110) REVERT: K 221 GLU cc_start: 0.8991 (tp30) cc_final: 0.8484 (tp30) REVERT: K 222 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8578 (mp0) REVERT: K 224 TYR cc_start: 0.9322 (m-10) cc_final: 0.9041 (m-10) REVERT: K 225 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8789 (mm110) REVERT: L 248 TYR cc_start: 0.9154 (p90) cc_final: 0.8453 (p90) REVERT: M 112 ARG cc_start: 0.8846 (tmm-80) cc_final: 0.8592 (tmm-80) outliers start: 19 outliers final: 7 residues processed: 287 average time/residue: 1.4862 time to fit residues: 463.2541 Evaluate side-chains 270 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 262 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 42 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 124 optimal weight: 30.0000 chunk 134 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 104 GLN G 38 ASN G 73 ASN H 44 GLN H 46 HIS ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15952 Z= 0.245 Angle : 0.650 13.365 22788 Z= 0.366 Chirality : 0.039 0.176 2606 Planarity : 0.004 0.048 1879 Dihedral : 29.345 106.910 4456 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.28 % Allowed : 17.73 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.24), residues: 1136 helix: 1.55 (0.19), residues: 691 sheet: 0.48 (0.48), residues: 127 loop : -1.04 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP M 76 HIS 0.004 0.001 HIS B 75 PHE 0.023 0.002 PHE M 44 TYR 0.046 0.002 TYR L 10 ARG 0.006 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 266 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8836 (mtt-85) cc_final: 0.8616 (mtt90) REVERT: D 90 GLU cc_start: 0.8520 (mp0) cc_final: 0.8055 (mp0) REVERT: E 120 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8354 (mtm) REVERT: G 94 ASN cc_start: 0.9220 (t0) cc_final: 0.8912 (t160) REVERT: H 31 LYS cc_start: 0.7898 (mppt) cc_final: 0.7559 (mptt) REVERT: H 65 ASP cc_start: 0.8545 (t70) cc_final: 0.8236 (t0) REVERT: K 69 ASN cc_start: 0.9007 (t0) cc_final: 0.8645 (t160) REVERT: K 88 HIS cc_start: 0.9242 (m-70) cc_final: 0.8760 (m-70) REVERT: K 111 THR cc_start: 0.9478 (t) cc_final: 0.9239 (t) REVERT: K 121 MET cc_start: 0.8777 (ppp) cc_final: 0.8449 (ppp) REVERT: K 221 GLU cc_start: 0.8972 (tp30) cc_final: 0.8394 (tp30) REVERT: K 224 TYR cc_start: 0.9373 (m-10) cc_final: 0.9064 (m-10) REVERT: K 225 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8803 (mm110) REVERT: M 69 TYR cc_start: 0.7756 (p90) cc_final: 0.7516 (p90) REVERT: M 76 TRP cc_start: 0.8559 (m100) cc_final: 0.8310 (m100) REVERT: M 112 ARG cc_start: 0.8821 (tmm-80) cc_final: 0.8551 (tmm-80) outliers start: 32 outliers final: 13 residues processed: 275 average time/residue: 1.4949 time to fit residues: 446.1313 Evaluate side-chains 273 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 259 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 62 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 38 ASN C 104 GLN G 38 ASN H 44 GLN ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15952 Z= 0.393 Angle : 0.681 12.993 22788 Z= 0.383 Chirality : 0.041 0.170 2606 Planarity : 0.004 0.045 1879 Dihedral : 29.687 110.879 4456 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.28 % Allowed : 18.75 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.15 (0.24), residues: 1136 helix: 1.62 (0.19), residues: 691 sheet: 0.63 (0.49), residues: 123 loop : -1.03 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 258 HIS 0.004 0.001 HIS B 75 PHE 0.019 0.002 PHE M 44 TYR 0.043 0.002 TYR L 10 ARG 0.006 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 264 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8585 (m-30) cc_final: 0.8370 (m-30) REVERT: C 75 LYS cc_start: 0.9310 (mttm) cc_final: 0.9077 (mttm) REVERT: D 90 GLU cc_start: 0.8577 (mp0) cc_final: 0.8118 (mp0) REVERT: E 120 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8527 (mtp) REVERT: G 94 ASN cc_start: 0.9274 (t0) cc_final: 0.8986 (t160) REVERT: H 31 LYS cc_start: 0.7939 (mppt) cc_final: 0.7630 (mptt) REVERT: H 65 ASP cc_start: 0.8594 (t70) cc_final: 0.8295 (t0) REVERT: K 69 ASN cc_start: 0.9034 (t0) cc_final: 0.8687 (t160) REVERT: K 88 HIS cc_start: 0.9251 (m-70) cc_final: 0.8714 (m-70) REVERT: K 121 MET cc_start: 0.8779 (ppp) cc_final: 0.8402 (ppp) REVERT: K 195 TYR cc_start: 0.8411 (t80) cc_final: 0.7981 (t80) REVERT: K 221 GLU cc_start: 0.9034 (tp30) cc_final: 0.8317 (tp30) REVERT: K 224 TYR cc_start: 0.9434 (m-10) cc_final: 0.9089 (m-10) REVERT: K 225 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8840 (mm110) REVERT: M 69 TYR cc_start: 0.7879 (p90) cc_final: 0.7559 (p90) REVERT: M 71 PHE cc_start: 0.8471 (t80) cc_final: 0.7751 (t80) outliers start: 32 outliers final: 17 residues processed: 274 average time/residue: 1.5651 time to fit residues: 463.8735 Evaluate side-chains 274 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 256 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 40.0000 chunk 75 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 113 optimal weight: 40.0000 chunk 91 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 104 GLN E 125 GLN G 38 ASN H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 HIS ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15952 Z= 0.328 Angle : 0.671 13.913 22788 Z= 0.376 Chirality : 0.040 0.175 2606 Planarity : 0.004 0.044 1879 Dihedral : 29.582 113.705 4456 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.28 % Allowed : 20.18 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.23 (0.25), residues: 1136 helix: 1.69 (0.19), residues: 691 sheet: 0.43 (0.48), residues: 127 loop : -0.95 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 258 HIS 0.004 0.001 HIS B 75 PHE 0.021 0.002 PHE M 44 TYR 0.040 0.002 TYR L 10 ARG 0.006 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 264 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 LYS cc_start: 0.9295 (mttm) cc_final: 0.9044 (mttm) REVERT: E 120 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8534 (mtp) REVERT: G 94 ASN cc_start: 0.9251 (t0) cc_final: 0.8996 (t0) REVERT: H 65 ASP cc_start: 0.8597 (t70) cc_final: 0.8297 (t0) REVERT: K 69 ASN cc_start: 0.8998 (t0) cc_final: 0.8679 (t160) REVERT: K 75 THR cc_start: 0.9121 (m) cc_final: 0.8878 (p) REVERT: K 88 HIS cc_start: 0.9179 (m90) cc_final: 0.8936 (m90) REVERT: K 121 MET cc_start: 0.8828 (ppp) cc_final: 0.8462 (ppp) REVERT: K 154 ASP cc_start: 0.8491 (t0) cc_final: 0.8181 (t0) REVERT: K 221 GLU cc_start: 0.9010 (tp30) cc_final: 0.8273 (tp30) REVERT: K 224 TYR cc_start: 0.9439 (m-10) cc_final: 0.9022 (m-10) REVERT: K 225 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8859 (mm110) REVERT: M 67 ASP cc_start: 0.9449 (t0) cc_final: 0.8958 (p0) REVERT: M 69 TYR cc_start: 0.7911 (p90) cc_final: 0.7598 (p90) REVERT: M 76 TRP cc_start: 0.8714 (m100) cc_final: 0.8456 (m100) outliers start: 32 outliers final: 20 residues processed: 276 average time/residue: 1.5374 time to fit residues: 459.5186 Evaluate side-chains 275 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 254 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 83 CYS Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 0.6980 chunk 119 optimal weight: 0.0020 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 110 optimal weight: 30.0000 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 104 GLN E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15952 Z= 0.191 Angle : 0.659 18.908 22788 Z= 0.367 Chirality : 0.038 0.341 2606 Planarity : 0.004 0.045 1879 Dihedral : 29.144 114.131 4456 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.84 % Allowed : 23.36 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.47 (0.25), residues: 1136 helix: 1.92 (0.19), residues: 691 sheet: 0.36 (0.49), residues: 127 loop : -0.86 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 258 HIS 0.004 0.001 HIS B 75 PHE 0.020 0.001 PHE M 44 TYR 0.032 0.002 TYR L 10 ARG 0.007 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 273 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7940 (mm-30) REVERT: B 95 ARG cc_start: 0.8791 (mtt-85) cc_final: 0.8514 (mtt90) REVERT: C 75 LYS cc_start: 0.9301 (mttm) cc_final: 0.9081 (mttm) REVERT: C 110 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8474 (p0) REVERT: E 120 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8542 (mtp) REVERT: H 31 LYS cc_start: 0.7938 (mppt) cc_final: 0.7663 (mptt) REVERT: H 65 ASP cc_start: 0.8544 (t70) cc_final: 0.8283 (t0) REVERT: K 69 ASN cc_start: 0.8969 (t0) cc_final: 0.8266 (m-40) REVERT: K 75 THR cc_start: 0.9040 (m) cc_final: 0.8730 (p) REVERT: K 88 HIS cc_start: 0.9191 (m90) cc_final: 0.8859 (m90) REVERT: K 121 MET cc_start: 0.8872 (ppp) cc_final: 0.8435 (ppp) REVERT: K 154 ASP cc_start: 0.8573 (t0) cc_final: 0.8256 (t0) REVERT: K 195 TYR cc_start: 0.8449 (t80) cc_final: 0.8244 (t80) REVERT: K 221 GLU cc_start: 0.8914 (tp30) cc_final: 0.8246 (tp30) REVERT: K 224 TYR cc_start: 0.9408 (m-10) cc_final: 0.9121 (m-10) REVERT: K 225 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8846 (mm110) REVERT: K 240 MET cc_start: 0.6686 (ttt) cc_final: 0.6234 (tpp) REVERT: M 67 ASP cc_start: 0.9397 (t0) cc_final: 0.9031 (p0) REVERT: M 69 TYR cc_start: 0.7928 (p90) cc_final: 0.7620 (p90) REVERT: M 76 TRP cc_start: 0.8720 (m100) cc_final: 0.8444 (m100) REVERT: M 108 VAL cc_start: 0.8043 (t) cc_final: 0.7721 (p) outliers start: 18 outliers final: 9 residues processed: 282 average time/residue: 1.5489 time to fit residues: 473.5989 Evaluate side-chains 268 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 257 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 83 CYS Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 0.0270 chunk 14 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 132 optimal weight: 50.0000 chunk 82 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 104 GLN G 38 ASN G 73 ASN G 112 GLN H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 15952 Z= 0.461 Angle : 0.724 18.849 22788 Z= 0.400 Chirality : 0.043 0.177 2606 Planarity : 0.004 0.043 1879 Dihedral : 29.782 112.661 4456 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.97 % Allowed : 23.87 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.22 (0.25), residues: 1136 helix: 1.69 (0.19), residues: 690 sheet: 0.67 (0.47), residues: 131 loop : -1.09 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 258 HIS 0.005 0.001 HIS K 179 PHE 0.021 0.002 PHE M 44 TYR 0.038 0.002 TYR L 10 ARG 0.007 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8919 (mtp85) cc_final: 0.8679 (mtp85) REVERT: C 75 LYS cc_start: 0.9289 (mttm) cc_final: 0.9071 (mttm) REVERT: C 110 ASN cc_start: 0.8968 (OUTLIER) cc_final: 0.8416 (p0) REVERT: D 73 GLU cc_start: 0.8423 (tp30) cc_final: 0.8103 (tp30) REVERT: D 76 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.8338 (mtm110) REVERT: D 90 GLU cc_start: 0.8564 (mp0) cc_final: 0.8041 (mp0) REVERT: E 120 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8560 (mtp) REVERT: E 125 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7819 (mp10) REVERT: H 31 LYS cc_start: 0.8037 (mppt) cc_final: 0.7792 (mptt) REVERT: H 65 ASP cc_start: 0.8654 (t70) cc_final: 0.8311 (t0) REVERT: K 69 ASN cc_start: 0.8973 (t0) cc_final: 0.8224 (m-40) REVERT: K 75 THR cc_start: 0.9177 (m) cc_final: 0.8888 (p) REVERT: K 88 HIS cc_start: 0.9174 (m90) cc_final: 0.8907 (m90) REVERT: K 121 MET cc_start: 0.8892 (ppp) cc_final: 0.8372 (ppp) REVERT: K 154 ASP cc_start: 0.8636 (t0) cc_final: 0.8321 (t0) REVERT: K 221 GLU cc_start: 0.8951 (tp30) cc_final: 0.8340 (tp30) REVERT: K 224 TYR cc_start: 0.9468 (m-10) cc_final: 0.9055 (m-10) REVERT: K 225 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8848 (mm110) REVERT: K 240 MET cc_start: 0.6931 (ttt) cc_final: 0.6483 (tpp) REVERT: M 67 ASP cc_start: 0.9362 (t0) cc_final: 0.9029 (p0) REVERT: M 69 TYR cc_start: 0.7946 (p90) cc_final: 0.7612 (p90) REVERT: M 76 TRP cc_start: 0.8809 (m100) cc_final: 0.8528 (m100) REVERT: M 78 PHE cc_start: 0.9243 (m-80) cc_final: 0.9034 (m-80) outliers start: 29 outliers final: 19 residues processed: 257 average time/residue: 1.6812 time to fit residues: 467.9700 Evaluate side-chains 259 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 83 CYS Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 104 GLN H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15952 Z= 0.199 Angle : 0.681 21.737 22788 Z= 0.375 Chirality : 0.038 0.181 2606 Planarity : 0.004 0.045 1879 Dihedral : 29.179 115.516 4456 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.74 % Allowed : 25.31 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.43 (0.25), residues: 1136 helix: 1.92 (0.19), residues: 684 sheet: 0.37 (0.47), residues: 135 loop : -0.94 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 258 HIS 0.003 0.001 HIS B 75 PHE 0.014 0.001 PHE E 67 TYR 0.032 0.002 TYR L 10 ARG 0.006 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 261 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8841 (mtp85) cc_final: 0.8574 (mtp85) REVERT: C 75 LYS cc_start: 0.9295 (mttm) cc_final: 0.9072 (mttm) REVERT: C 110 ASN cc_start: 0.8889 (t0) cc_final: 0.8475 (p0) REVERT: D 90 GLU cc_start: 0.8442 (mp0) cc_final: 0.7864 (mp0) REVERT: E 81 ASP cc_start: 0.8101 (p0) cc_final: 0.7777 (p0) REVERT: E 120 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8592 (mtp) REVERT: H 31 LYS cc_start: 0.8004 (mppt) cc_final: 0.7775 (mptt) REVERT: H 65 ASP cc_start: 0.8587 (t70) cc_final: 0.8342 (t0) REVERT: H 105 LYS cc_start: 0.8662 (ttmm) cc_final: 0.8408 (mtpp) REVERT: K 69 ASN cc_start: 0.8919 (t0) cc_final: 0.8325 (m-40) REVERT: K 75 THR cc_start: 0.9090 (m) cc_final: 0.8789 (p) REVERT: K 88 HIS cc_start: 0.9177 (m90) cc_final: 0.8920 (m90) REVERT: K 121 MET cc_start: 0.8877 (ppp) cc_final: 0.8358 (ppp) REVERT: K 144 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8373 (mm-40) REVERT: K 154 ASP cc_start: 0.8565 (t0) cc_final: 0.8270 (t0) REVERT: K 221 GLU cc_start: 0.8909 (tp30) cc_final: 0.8402 (tp30) REVERT: K 224 TYR cc_start: 0.9407 (m-10) cc_final: 0.9114 (m-10) REVERT: K 225 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8890 (mm110) REVERT: K 240 MET cc_start: 0.6709 (ttt) cc_final: 0.6236 (tpp) REVERT: M 69 TYR cc_start: 0.7925 (p90) cc_final: 0.7639 (p90) outliers start: 17 outliers final: 10 residues processed: 271 average time/residue: 1.5582 time to fit residues: 457.9217 Evaluate side-chains 274 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 263 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 83 CYS Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 104 GLN D 106 HIS G 38 ASN H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 15952 Z= 0.445 Angle : 0.741 19.856 22788 Z= 0.406 Chirality : 0.043 0.170 2606 Planarity : 0.005 0.099 1879 Dihedral : 29.747 114.223 4456 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.87 % Allowed : 25.72 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.18 (0.25), residues: 1136 helix: 1.70 (0.19), residues: 684 sheet: 0.34 (0.47), residues: 131 loop : -1.02 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP M 76 HIS 0.006 0.001 HIS K 179 PHE 0.016 0.002 PHE M 78 TYR 0.036 0.002 TYR L 10 ARG 0.012 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8926 (mtp85) cc_final: 0.8664 (mtp85) REVERT: C 75 LYS cc_start: 0.9325 (mttm) cc_final: 0.9090 (mttm) REVERT: C 110 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8381 (p0) REVERT: E 120 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8548 (mtp) REVERT: H 31 LYS cc_start: 0.8042 (mppt) cc_final: 0.7806 (mptt) REVERT: H 65 ASP cc_start: 0.8659 (t70) cc_final: 0.8313 (t0) REVERT: K 69 ASN cc_start: 0.8886 (t0) cc_final: 0.8295 (m-40) REVERT: K 75 THR cc_start: 0.9132 (m) cc_final: 0.8825 (p) REVERT: K 88 HIS cc_start: 0.9167 (m90) cc_final: 0.8908 (m90) REVERT: K 121 MET cc_start: 0.8964 (ppp) cc_final: 0.8475 (ppp) REVERT: K 144 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8379 (mm-40) REVERT: K 154 ASP cc_start: 0.8634 (t0) cc_final: 0.8323 (t0) REVERT: K 221 GLU cc_start: 0.8968 (tp30) cc_final: 0.8489 (tp30) REVERT: K 224 TYR cc_start: 0.9433 (m-10) cc_final: 0.9017 (m-10) REVERT: K 225 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8919 (mm110) REVERT: K 240 MET cc_start: 0.7002 (ttt) cc_final: 0.6553 (tpp) REVERT: L 20 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7368 (pm20) REVERT: M 69 TYR cc_start: 0.7853 (p90) cc_final: 0.7516 (p90) REVERT: M 108 VAL cc_start: 0.8219 (t) cc_final: 0.7718 (p) outliers start: 28 outliers final: 17 residues processed: 262 average time/residue: 1.5267 time to fit residues: 434.2416 Evaluate side-chains 256 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 125 optimal weight: 50.0000 chunk 108 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 104 GLN E 125 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15952 Z= 0.358 Angle : 0.735 20.302 22788 Z= 0.401 Chirality : 0.041 0.192 2606 Planarity : 0.004 0.051 1879 Dihedral : 29.683 116.469 4456 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.84 % Allowed : 26.54 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.14 (0.25), residues: 1136 helix: 1.70 (0.19), residues: 684 sheet: 0.49 (0.49), residues: 121 loop : -1.13 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP M 76 HIS 0.006 0.001 HIS D 106 PHE 0.016 0.002 PHE M 78 TYR 0.035 0.002 TYR L 10 ARG 0.014 0.001 ARG K 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8876 (mtp85) cc_final: 0.8604 (mtp85) REVERT: C 75 LYS cc_start: 0.9293 (mttm) cc_final: 0.9066 (mttm) REVERT: C 110 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8391 (p0) REVERT: E 81 ASP cc_start: 0.8322 (p0) cc_final: 0.8025 (p0) REVERT: E 120 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8586 (mtp) REVERT: H 65 ASP cc_start: 0.8645 (t70) cc_final: 0.8338 (t0) REVERT: K 69 ASN cc_start: 0.8852 (t0) cc_final: 0.8288 (m-40) REVERT: K 75 THR cc_start: 0.9164 (m) cc_final: 0.8854 (p) REVERT: K 88 HIS cc_start: 0.9179 (m90) cc_final: 0.8924 (m90) REVERT: K 121 MET cc_start: 0.8912 (ppp) cc_final: 0.8435 (ppp) REVERT: K 144 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8390 (mm-40) REVERT: K 154 ASP cc_start: 0.8625 (t0) cc_final: 0.8312 (t0) REVERT: K 221 GLU cc_start: 0.8923 (tp30) cc_final: 0.8354 (tp30) REVERT: K 224 TYR cc_start: 0.9421 (m-10) cc_final: 0.9039 (m-10) REVERT: K 225 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8888 (mm110) REVERT: K 240 MET cc_start: 0.6953 (ttt) cc_final: 0.6500 (tpp) REVERT: M 69 TYR cc_start: 0.7849 (p90) cc_final: 0.7526 (p90) outliers start: 18 outliers final: 11 residues processed: 256 average time/residue: 1.6031 time to fit residues: 450.3162 Evaluate side-chains 251 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 238 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 104 GLN D 44 GLN G 73 ASN H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.096728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.057479 restraints weight = 137102.919| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.54 r_work: 0.2574 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 71 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 71 | |-----------------------------------------------------------------------------| r_final: 0.2582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15952 Z= 0.209 Angle : 0.734 21.948 22788 Z= 0.396 Chirality : 0.039 0.191 2606 Planarity : 0.004 0.047 1879 Dihedral : 29.614 118.325 4456 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.43 % Allowed : 26.74 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.23 (0.25), residues: 1136 helix: 1.77 (0.20), residues: 684 sheet: 0.48 (0.49), residues: 121 loop : -1.07 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.005 TRP M 76 HIS 0.004 0.001 HIS B 75 PHE 0.024 0.002 PHE M 44 TYR 0.032 0.002 TYR L 10 ARG 0.014 0.001 ARG K 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6566.60 seconds wall clock time: 118 minutes 29.32 seconds (7109.32 seconds total)