Starting phenix.real_space_refine on Thu Aug 6 05:16:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwm_47255/08_2026/9dwm_47255.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwm_47255/08_2026/9dwm_47255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dwm_47255/08_2026/9dwm_47255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwm_47255/08_2026/9dwm_47255.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwm_47255/08_2026/9dwm_47255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwm_47255/08_2026/9dwm_47255.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 1.000 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 3362 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 P 289 5.49 5 C 5930 2.51 5 N 2155 2.21 5 O 2801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11175 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 482 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 14, 'TYR:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 6, 'PHE:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 192 Chain: "B" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 382 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ARG:plan': 10, 'TYR:plan': 4, 'GLU:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 134 Chain: "C" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 531 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 249 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 11, 'GLN:plan1': 4, 'PHE:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 6, 'TYR:plan': 3, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 156 Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 460 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 6, 'TYR:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 139 Chain: "E" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 482 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 14, 'TYR:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 6, 'PHE:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 192 Chain: "F" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 382 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ARG:plan': 10, 'TYR:plan': 4, 'GLU:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 134 Chain: "G" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 501 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 5, 'TRANS': 96} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 10, 'GLN:plan1': 4, 'PHE:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 6, 'TYR:plan': 3, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 151 Chain: "H" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 450 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 2, 'TRANS': 88} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 134 Chain: "I" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2566 Classifications: {'DNA': 126} Link IDs: {'rna3p': 125} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 17} Chain: "L" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 1583 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 282} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 306} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1042 Unresolved non-hydrogen angles: 1314 Unresolved non-hydrogen dihedrals: 872 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'ASN:plan1': 12, 'ASP:plan': 21, 'GLU:plan': 26, 'PHE:plan': 14, 'GLN:plan1': 11, 'HIS:plan': 9, 'TYR:plan': 12, 'ARG:plan': 18, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 559 Time building chain proxies: 2.52, per 1000 atoms: 0.23 Number of scatterers: 11175 At special positions: 0 Unit cell: (101.85, 118.34, 166.84, 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) P 289 15.00 O 2801 8.00 N 2155 7.00 C 5930 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: 0.73 Conformation dependent library (CDL) restraints added in 507.6 milliseconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1986 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 70.2% alpha, 3.8% beta 143 base pairs and 229 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 50 through 56 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.677A pdb=" N HIS A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.169A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 48 through 75 removed outlier: 4.323A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.156A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.717A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 85 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.797A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.922A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.021A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.557A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 4.525A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 74 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.973A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'L' and resid 12 through 29 Processing helix chain 'L' and resid 32 through 49 removed outlier: 4.011A pdb=" N ALA L 38 " --> pdb=" O HIS L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 61 removed outlier: 3.627A pdb=" N LYS L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 80 Processing helix chain 'L' and resid 82 through 91 Processing helix chain 'L' and resid 91 through 103 removed outlier: 3.825A pdb=" N VAL L 103 " --> pdb=" O PHE L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 117 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 129 through 132 Processing helix chain 'L' and resid 133 through 142 Processing helix chain 'L' and resid 142 through 148 Processing helix chain 'L' and resid 152 through 170 Processing helix chain 'L' and resid 179 through 184 Processing helix chain 'L' and resid 209 through 221 removed outlier: 3.600A pdb=" N VAL L 221 " --> pdb=" O GLN L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 274 removed outlier: 4.452A pdb=" N TYR L 266 " --> pdb=" O LYS L 262 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N CYS L 267 " --> pdb=" O ASP L 263 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY L 274 " --> pdb=" O LEU L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 275 through 289 Processing helix chain 'L' and resid 315 through 323 removed outlier: 3.599A pdb=" N ILE L 323 " --> pdb=" O ILE L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 329 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.278A 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 'B' and resid 96 through 97 removed outlier: 7.105A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.232A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.190A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 150 through 151 Processing sheet with id=AA7, first strand: chain 'L' and resid 174 through 177 removed outlier: 6.333A pdb=" N MET L 191 " --> pdb=" O ASP L 256 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ARG L 258 " --> pdb=" O MET L 191 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL L 193 " --> pdb=" O ARG L 258 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL L 238 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N THR L 227 " --> pdb=" O VAL L 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 291 through 293 527 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 229 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.29: 1355 1.29 - 1.37: 2767 1.37 - 1.46: 2322 1.46 - 1.54: 4727 1.54 - 1.62: 712 Bond restraints: 11883 Sorted by residual: bond pdb=" P DT K 129 " pdb=" OP3 DT K 129 " ideal model delta sigma weight residual 1.480 1.601 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" C1' DC K 139 " pdb=" N1 DC K 139 " ideal model delta sigma weight residual 1.468 1.542 -0.074 1.40e-02 5.10e+03 2.79e+01 bond pdb=" C3' DG I 55 " pdb=" C2' DG I 55 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DG I 114 " pdb=" C2' DG I 114 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DC K 130 " pdb=" C2' DC K 130 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 ... (remaining 11878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 16353 1.60 - 3.20: 1101 3.20 - 4.81: 53 4.81 - 6.41: 9 6.41 - 8.01: 7 Bond angle restraints: 17523 Sorted by residual: angle pdb=" O4' DA J 14 " pdb=" C4' DA J 14 " pdb=" C3' DA J 14 " ideal model delta sigma weight residual 106.00 102.75 3.25 6.00e-01 2.78e+00 2.94e+01 angle pdb=" O4' DT I 48 " pdb=" C4' DT I 48 " pdb=" C3' DT I 48 " ideal model delta sigma weight residual 106.00 102.78 3.22 6.00e-01 2.78e+00 2.88e+01 angle pdb=" O4' DA J 19 " pdb=" C4' DA J 19 " pdb=" C3' DA J 19 " ideal model delta sigma weight residual 106.00 102.80 3.20 6.00e-01 2.78e+00 2.85e+01 angle pdb=" C3' DA J 6 " pdb=" O3' DA J 6 " pdb=" P DT J 7 " ideal model delta sigma weight residual 119.70 125.69 -5.99 1.20e+00 6.94e-01 2.49e+01 angle pdb=" O4' DG J 120 " pdb=" C4' DG J 120 " pdb=" C3' DG J 120 " ideal model delta sigma weight residual 106.00 103.07 2.93 6.00e-01 2.78e+00 2.39e+01 ... (remaining 17518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.20: 4587 28.20 - 56.41: 1359 56.41 - 84.61: 217 84.61 - 112.81: 5 112.81 - 141.02: 2 Dihedral angle restraints: 6170 sinusoidal: 3129 harmonic: 3041 Sorted by residual: dihedral pdb=" C4' DG J 82 " pdb=" C3' DG J 82 " pdb=" O3' DG J 82 " pdb=" P DT J 83 " ideal model delta sinusoidal sigma weight residual 220.00 78.98 141.02 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 83.85 136.15 1 3.50e+01 8.16e-04 1.35e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 6167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2131 0.131 - 0.263: 14 0.263 - 0.394: 0 0.394 - 0.526: 1 0.526 - 0.657: 3 Chirality restraints: 2149 Sorted by residual: chirality pdb=" P DT J 7 " pdb=" OP1 DT J 7 " pdb=" OP2 DT J 7 " pdb=" O5' DT J 7 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P DA I 69 " pdb=" OP1 DA I 69 " pdb=" OP2 DA I 69 " pdb=" O5' DA I 69 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.59 2.00e-01 2.50e+01 8.71e+00 chirality pdb=" P DC I 111 " pdb=" OP1 DC I 111 " pdb=" OP2 DC I 111 " pdb=" O5' DC I 111 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.58 2.00e-01 2.50e+01 8.28e+00 ... (remaining 2146 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 7 " -0.022 2.00e-02 2.50e+03 1.12e-02 3.13e+00 pdb=" N1 DT J 7 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DT J 7 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT J 7 " 0.017 2.00e-02 2.50e+03 pdb=" N3 DT J 7 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT J 7 " -0.008 2.00e-02 2.50e+03 pdb=" O4 DT J 7 " -0.012 2.00e-02 2.50e+03 pdb=" C5 DT J 7 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT J 7 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DT J 7 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 91 " -0.020 2.00e-02 2.50e+03 9.39e-03 2.42e+00 pdb=" N9 DA I 91 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DA I 91 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 91 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 91 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 91 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 91 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 91 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 91 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 91 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 91 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " -0.022 2.00e-02 2.50e+03 9.11e-03 2.28e+00 pdb=" N9 DA I 39 " 0.017 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " 0.003 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3579 2.85 - 3.36: 10383 3.36 - 3.88: 21949 3.88 - 4.39: 22251 4.39 - 4.90: 30091 Nonbonded interactions: 88253 Sorted by model distance: nonbonded pdb=" N VAL A 117 " pdb=" OP2 DG I 71 " model vdw 2.339 3.120 nonbonded pdb=" OP1 DC K 130 " pdb=" N THR L 67 " model vdw 2.369 3.120 nonbonded pdb=" O ILE L 298 " pdb=" N LEU L 311 " model vdw 2.377 3.120 nonbonded pdb=" O GLU L 26 " pdb=" N ALA L 32 " model vdw 2.399 3.120 nonbonded pdb=" O THR G 16 " pdb=" N ARG G 20 " model vdw 2.412 3.120 ... (remaining 88248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.350 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 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 : 0.006 0.121 11883 Z= 0.584 Angle : 0.787 8.008 17523 Z= 0.725 Chirality : 0.052 0.657 2149 Planarity : 0.002 0.011 1344 Dihedral : 30.430 141.016 4184 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.26), residues: 1045 helix: 2.56 (0.20), residues: 680 sheet: 2.96 (0.80), residues: 35 loop : -0.27 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.58 (11883) covalent geometry : angle 0.78659 / 0.73 (17523) hydrogen bonds : bond 0.11862 / 9.03 ( 894) hydrogen bonds : angle 4.31793 / 3.34 ( 2291) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0492 time to fit residues: 1.8278 Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 50.0000 chunk 91 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.059466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.035709 restraints weight = 124455.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.035564 restraints weight = 74842.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035869 restraints weight = 50608.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.036078 restraints weight = 39704.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.036144 restraints weight = 34335.284| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.0550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11883 Z= 0.218 Angle : 0.642 7.212 17523 Z= 0.413 Chirality : 0.046 0.211 2149 Planarity : 0.003 0.013 1344 Dihedral : 30.484 141.781 4184 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.27), residues: 1045 helix: 2.44 (0.19), residues: 719 sheet: 2.90 (0.84), residues: 35 loop : -0.76 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.22 (11883) covalent geometry : angle 0.64217 / 0.41 (17523) hydrogen bonds : bond 0.06233 / 4.74 ( 894) hydrogen bonds : angle 3.96946 / 3.09 ( 2291) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.307 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0479 time to fit residues: 1.8129 Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 26 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 28 optimal weight: 30.0000 chunk 5 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.058674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.034457 restraints weight = 125746.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.034897 restraints weight = 69274.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.035167 restraints weight = 47183.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.035268 restraints weight = 37292.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.035454 restraints weight = 33346.144| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 11883 Z= 0.269 Angle : 0.674 6.584 17523 Z= 0.437 Chirality : 0.046 0.201 2149 Planarity : 0.003 0.013 1344 Dihedral : 30.580 141.666 4184 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.26), residues: 1045 helix: 1.85 (0.19), residues: 718 sheet: 2.61 (0.85), residues: 35 loop : -1.02 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.27 (11883) covalent geometry : angle 0.67428 / 0.44 (17523) hydrogen bonds : bond 0.08234 / 6.31 ( 894) hydrogen bonds : angle 4.26539 / 3.33 ( 2291) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.297 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0490 time to fit residues: 1.8211 Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 9.9990 chunk 116 optimal weight: 50.0000 chunk 35 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 22 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 114 optimal weight: 50.0000 chunk 117 optimal weight: 40.0000 chunk 44 optimal weight: 10.0000 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.057654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.033709 restraints weight = 127919.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.033965 restraints weight = 73242.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.034206 restraints weight = 51075.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.034285 restraints weight = 41279.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.034449 restraints weight = 37436.319| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11883 Z= 0.379 Angle : 0.834 8.414 17523 Z= 0.521 Chirality : 0.053 0.228 2149 Planarity : 0.005 0.016 1344 Dihedral : 30.977 140.234 4184 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1045 helix: 0.51 (0.19), residues: 714 sheet: 1.42 (0.79), residues: 35 loop : -1.37 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.38 (11883) covalent geometry : angle 0.83424 / 0.52 (17523) hydrogen bonds : bond 0.11901 / 9.09 ( 894) hydrogen bonds : angle 5.50070 / 4.29 ( 2291) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.205 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0481 time to fit residues: 1.6867 Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 102 optimal weight: 30.0000 chunk 118 optimal weight: 50.0000 chunk 119 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 100 optimal weight: 50.0000 chunk 9 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.057930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.035282 restraints weight = 141025.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.035848 restraints weight = 74001.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.036211 restraints weight = 47807.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.036400 restraints weight = 35465.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036553 restraints weight = 29535.305| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11883 Z= 0.267 Angle : 0.699 7.294 17523 Z= 0.438 Chirality : 0.048 0.207 2149 Planarity : 0.003 0.013 1344 Dihedral : 30.987 139.766 4184 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.26), residues: 1045 helix: 1.13 (0.19), residues: 713 sheet: 1.27 (0.82), residues: 35 loop : -1.44 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.27 (11883) covalent geometry : angle 0.69912 / 0.44 (17523) hydrogen bonds : bond 0.07782 / 5.93 ( 894) hydrogen bonds : angle 4.56100 / 3.56 ( 2291) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.207 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0348 time to fit residues: 1.3605 Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 102 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 70 optimal weight: 50.0000 chunk 85 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.060374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.036744 restraints weight = 134908.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.037357 restraints weight = 71649.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.037726 restraints weight = 46615.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.037954 restraints weight = 35024.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.038111 restraints weight = 29354.546| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 11883 Z= 0.194 Angle : 0.616 7.494 17523 Z= 0.390 Chirality : 0.045 0.207 2149 Planarity : 0.003 0.011 1344 Dihedral : 30.858 139.218 4184 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.27), residues: 1045 helix: 2.26 (0.20), residues: 716 sheet: 1.06 (0.84), residues: 35 loop : -1.42 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.19 (11883) covalent geometry : angle 0.61621 / 0.39 (17523) hydrogen bonds : bond 0.05810 / 4.43 ( 894) hydrogen bonds : angle 3.74435 / 2.93 ( 2291) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.185 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0420 time to fit residues: 1.5074 Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 66 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 91 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.057781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.035204 restraints weight = 139642.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.035766 restraints weight = 73557.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.036129 restraints weight = 47507.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.036371 restraints weight = 35373.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036484 restraints weight = 29224.875| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 11883 Z= 0.262 Angle : 0.678 7.737 17523 Z= 0.428 Chirality : 0.047 0.215 2149 Planarity : 0.003 0.013 1344 Dihedral : 30.894 142.912 4184 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.27), residues: 1045 helix: 1.73 (0.19), residues: 720 sheet: 0.89 (0.85), residues: 35 loop : -1.59 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.26 (11883) covalent geometry : angle 0.67824 / 0.43 (17523) hydrogen bonds : bond 0.08251 / 6.29 ( 894) hydrogen bonds : angle 4.40174 / 3.44 ( 2291) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.292 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0482 time to fit residues: 1.7947 Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 83 optimal weight: 50.0000 chunk 113 optimal weight: 50.0000 chunk 121 optimal weight: 50.0000 chunk 96 optimal weight: 50.0000 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 80 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 104 optimal weight: 30.0000 overall best weight: 11.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.056884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.033462 restraints weight = 139026.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.034005 restraints weight = 69334.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.034351 restraints weight = 44182.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.034512 restraints weight = 33099.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.034685 restraints weight = 28161.045| |-----------------------------------------------------------------------------| r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 11883 Z= 0.384 Angle : 0.860 8.193 17523 Z= 0.532 Chirality : 0.054 0.231 2149 Planarity : 0.005 0.016 1344 Dihedral : 31.142 145.179 4184 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.26), residues: 1045 helix: 0.27 (0.19), residues: 698 sheet: 1.44 (1.00), residues: 27 loop : -1.75 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.38 (11883) covalent geometry : angle 0.86004 / 0.53 (17523) hydrogen bonds : bond 0.13125 / 10.01 ( 894) hydrogen bonds : angle 5.78707 / 4.51 ( 2291) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.279 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0478 time to fit residues: 1.7841 Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 80 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 126 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 29 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.058089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.035485 restraints weight = 138052.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.036067 restraints weight = 72455.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.036431 restraints weight = 46525.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.036662 restraints weight = 34626.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.036782 restraints weight = 28619.277| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 11883 Z= 0.194 Angle : 0.655 7.318 17523 Z= 0.409 Chirality : 0.047 0.230 2149 Planarity : 0.003 0.011 1344 Dihedral : 31.099 139.912 4184 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.27), residues: 1045 helix: 1.75 (0.20), residues: 698 sheet: 1.33 (1.05), residues: 27 loop : -1.60 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.19 (11883) covalent geometry : angle 0.65497 / 0.41 (17523) hydrogen bonds : bond 0.06646 / 5.05 ( 894) hydrogen bonds : angle 4.10421 / 3.20 ( 2291) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.241 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0338 time to fit residues: 1.2934 Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 116 optimal weight: 50.0000 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 97 optimal weight: 50.0000 chunk 83 optimal weight: 50.0000 chunk 46 optimal weight: 7.9990 chunk 124 optimal weight: 40.0000 chunk 37 optimal weight: 9.9990 chunk 110 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.057255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.034941 restraints weight = 142475.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.035510 restraints weight = 75805.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.035810 restraints weight = 49563.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.036058 restraints weight = 37257.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.036192 restraints weight = 30712.284| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 11883 Z= 0.298 Angle : 0.737 7.821 17523 Z= 0.459 Chirality : 0.049 0.236 2149 Planarity : 0.004 0.014 1344 Dihedral : 31.041 145.111 4184 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.26), residues: 1045 helix: 1.18 (0.20), residues: 698 sheet: 0.68 (1.02), residues: 29 loop : -1.72 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.30 (11883) covalent geometry : angle 0.73739 / 0.46 (17523) hydrogen bonds : bond 0.09529 / 7.26 ( 894) hydrogen bonds : angle 4.91583 / 3.83 ( 2291) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.163 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0425 time to fit residues: 1.5631 Evaluate side-chains 16 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 116 optimal weight: 40.0000 chunk 128 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.057789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.035292 restraints weight = 141773.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.035852 restraints weight = 74417.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.036227 restraints weight = 47928.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.036470 restraints weight = 35544.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.036593 restraints weight = 29255.686| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 11883 Z= 0.219 Angle : 0.658 7.504 17523 Z= 0.412 Chirality : 0.046 0.235 2149 Planarity : 0.003 0.011 1344 Dihedral : 31.015 142.849 4184 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.27), residues: 1045 helix: 1.79 (0.20), residues: 699 sheet: 0.73 (1.02), residues: 29 loop : -1.67 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.22 (11883) covalent geometry : angle 0.65821 / 0.41 (17523) hydrogen bonds : bond 0.06817 / 5.18 ( 894) hydrogen bonds : angle 4.23861 / 3.31 ( 2291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2382.71 seconds wall clock time: 41 minutes 14.94 seconds (2474.94 seconds total)